Starting phenix.real_space_refine on Sun Mar 10 23:21:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyr_27082/03_2024/8cyr_27082.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyr_27082/03_2024/8cyr_27082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyr_27082/03_2024/8cyr_27082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyr_27082/03_2024/8cyr_27082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyr_27082/03_2024/8cyr_27082.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyr_27082/03_2024/8cyr_27082.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.006 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 3744 2.51 5 N 1044 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5964 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "B" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "C" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "D" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "E" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "F" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "I" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "J" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "K" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "L" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "M" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "N" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Time building chain proxies: 3.56, per 1000 atoms: 0.60 Number of scatterers: 5964 At special positions: 0 Unit cell: (124.2, 82.08, 51.84, 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 1176 8.00 N 1044 7.00 C 3744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.2 seconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.193A pdb=" N ALA C 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA I 17 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA K 17 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 21 through 23 removed outlier: 6.361A pdb=" N THR A 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 45 removed outlier: 6.514A pdb=" N VAL A 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL E 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER E 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY A 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR E 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS A 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.472A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 55 removed outlier: 6.071A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR A 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR I 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR K 54 " --> pdb=" O VAL M 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 63 through 66 removed outlier: 6.788A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL E 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN A 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 71 through 72 removed outlier: 6.584A pdb=" N VAL A 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 77 removed outlier: 6.495A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 removed outlier: 6.251A pdb=" N SER C 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER I 87 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER K 87 " --> pdb=" O ILE M 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 18 removed outlier: 6.322A pdb=" N ALA D 17 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA J 17 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA L 17 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 21 through 23 removed outlier: 6.210A pdb=" N THR B 22 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 37 through 45 removed outlier: 6.106A pdb=" N LEU D 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY F 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LYS F 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER D 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS F 45 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR D 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY J 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LYS J 43 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 42 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS J 45 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 44 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU J 38 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLY L 41 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL J 40 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LYS L 43 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER J 42 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS L 45 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR J 44 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU L 38 " --> pdb=" O TYR N 39 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLY N 41 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL L 40 " --> pdb=" O GLY N 41 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS N 43 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER L 42 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LYS N 45 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR L 44 " --> pdb=" O LYS N 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.352A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 55 removed outlier: 5.829A pdb=" N THR D 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR B 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR J 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR L 54 " --> pdb=" O VAL N 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 66 removed outlier: 7.027A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL F 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN B 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 71 through 72 removed outlier: 6.778A pdb=" N VAL B 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.245A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 88 removed outlier: 6.098A pdb=" N SER D 87 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER B 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER J 87 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER L 87 " --> pdb=" O ILE N 88 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 420 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: 1.50 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1032 1.29 - 1.36: 924 1.36 - 1.42: 204 1.42 - 1.48: 972 1.48 - 1.55: 2844 Bond restraints: 5976 Sorted by residual: bond pdb=" CA GLY M 68 " pdb=" C GLY M 68 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.06e-02 8.90e+03 1.75e+00 bond pdb=" CA GLY L 68 " pdb=" C GLY L 68 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.06e-02 8.90e+03 1.71e+00 bond pdb=" CA GLY I 68 " pdb=" C GLY I 68 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.06e-02 8.90e+03 1.65e+00 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.06e-02 8.90e+03 1.65e+00 bond pdb=" CA GLY C 68 " pdb=" C GLY C 68 " ideal model delta sigma weight residual 1.522 1.508 0.013 1.06e-02 8.90e+03 1.62e+00 ... (remaining 5971 not shown) Histogram of bond angle deviations from ideal: 106.11 - 111.12: 2495 111.12 - 116.14: 1856 116.14 - 121.15: 1818 121.15 - 126.16: 1871 126.16 - 131.17: 12 Bond angle restraints: 8052 Sorted by residual: angle pdb=" N GLY B 73 " pdb=" CA GLY B 73 " pdb=" C GLY B 73 " ideal model delta sigma weight residual 110.63 116.20 -5.57 1.45e+00 4.76e-01 1.47e+01 angle pdb=" N GLY N 73 " pdb=" CA GLY N 73 " pdb=" C GLY N 73 " ideal model delta sigma weight residual 110.63 116.19 -5.56 1.45e+00 4.76e-01 1.47e+01 angle pdb=" N GLY I 73 " pdb=" CA GLY I 73 " pdb=" C GLY I 73 " ideal model delta sigma weight residual 110.63 116.18 -5.55 1.45e+00 4.76e-01 1.46e+01 angle pdb=" N GLY L 73 " pdb=" CA GLY L 73 " pdb=" C GLY L 73 " ideal model delta sigma weight residual 110.63 116.17 -5.54 1.45e+00 4.76e-01 1.46e+01 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 110.63 116.15 -5.52 1.45e+00 4.76e-01 1.45e+01 ... (remaining 8047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.22: 3011 7.22 - 14.44: 289 14.44 - 21.66: 144 21.66 - 28.88: 60 28.88 - 36.09: 24 Dihedral angle restraints: 3528 sinusoidal: 1188 harmonic: 2340 Sorted by residual: dihedral pdb=" N VAL N 15 " pdb=" CA VAL N 15 " pdb=" CB VAL N 15 " pdb=" CG1 VAL N 15 " ideal model delta sinusoidal sigma weight residual -180.00 -143.91 -36.09 3 1.50e+01 4.44e-03 6.23e+00 dihedral pdb=" N VAL A 15 " pdb=" CA VAL A 15 " pdb=" CB VAL A 15 " pdb=" CG1 VAL A 15 " ideal model delta sinusoidal sigma weight residual 180.00 -143.92 -36.08 3 1.50e+01 4.44e-03 6.22e+00 dihedral pdb=" N VAL C 15 " pdb=" CA VAL C 15 " pdb=" CB VAL C 15 " pdb=" CG1 VAL C 15 " ideal model delta sinusoidal sigma weight residual -180.00 -143.93 -36.07 3 1.50e+01 4.44e-03 6.22e+00 ... (remaining 3525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 458 0.024 - 0.048: 270 0.048 - 0.072: 148 0.072 - 0.096: 28 0.096 - 0.120: 164 Chirality restraints: 1068 Sorted by residual: chirality pdb=" CA ILE K 88 " pdb=" N ILE K 88 " pdb=" C ILE K 88 " pdb=" CB ILE K 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE L 88 " pdb=" N ILE L 88 " pdb=" C ILE L 88 " pdb=" CB ILE L 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 1065 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 19 " -0.003 2.00e-02 2.50e+03 5.88e-03 3.46e-01 pdb=" C ALA B 19 " 0.010 2.00e-02 2.50e+03 pdb=" O ALA B 19 " -0.004 2.00e-02 2.50e+03 pdb=" N GLU B 20 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 19 " 0.003 2.00e-02 2.50e+03 5.84e-03 3.42e-01 pdb=" C ALA A 19 " -0.010 2.00e-02 2.50e+03 pdb=" O ALA A 19 " 0.004 2.00e-02 2.50e+03 pdb=" N GLU A 20 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 19 " -0.003 2.00e-02 2.50e+03 5.84e-03 3.41e-01 pdb=" C ALA F 19 " 0.010 2.00e-02 2.50e+03 pdb=" O ALA F 19 " -0.004 2.00e-02 2.50e+03 pdb=" N GLU F 20 " -0.003 2.00e-02 2.50e+03 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 3919 3.10 - 3.55: 5594 3.55 - 4.00: 8726 4.00 - 4.45: 9048 4.45 - 4.90: 20137 Nonbonded interactions: 47424 Sorted by model distance: nonbonded pdb=" O ALA J 17 " pdb=" OG SER L 87 " model vdw 2.654 2.440 nonbonded pdb=" O ALA B 17 " pdb=" OG SER J 87 " model vdw 2.655 2.440 nonbonded pdb=" O ALA L 17 " pdb=" OG SER N 87 " model vdw 2.655 2.440 nonbonded pdb=" O ALA D 17 " pdb=" OG SER F 87 " model vdw 2.655 2.440 nonbonded pdb=" OG SER B 87 " pdb=" O ALA F 17 " model vdw 2.656 2.440 ... (remaining 47419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.640 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 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 : 0.003 0.017 5976 Z= 0.181 Angle : 0.625 5.568 8052 Z= 0.402 Chirality : 0.054 0.120 1068 Planarity : 0.002 0.006 984 Dihedral : 8.968 36.094 2040 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.00 % Allowed : 4.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.37 (0.26), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.004 0.001 PHE E 94 TYR 0.006 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 VAL cc_start: 0.6713 (OUTLIER) cc_final: 0.5594 (t) REVERT: D 15 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.6550 (t) REVERT: F 15 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6061 (t) REVERT: I 15 VAL cc_start: 0.5408 (OUTLIER) cc_final: 0.5193 (t) REVERT: J 15 VAL cc_start: 0.7262 (OUTLIER) cc_final: 0.6373 (t) REVERT: K 15 VAL cc_start: 0.5777 (OUTLIER) cc_final: 0.5315 (t) REVERT: L 38 LEU cc_start: 0.7526 (mp) cc_final: 0.6892 (mp) REVERT: L 72 THR cc_start: 0.7717 (m) cc_final: 0.7404 (t) REVERT: L 79 GLN cc_start: 0.7377 (mt0) cc_final: 0.7116 (mt0) REVERT: N 39 TYR cc_start: 0.6986 (t80) cc_final: 0.6636 (t80) outliers start: 12 outliers final: 2 residues processed: 210 average time/residue: 0.2277 time to fit residues: 58.2768 Evaluate side-chains 76 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 42 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 5976 Z= 0.660 Angle : 1.034 7.152 8052 Z= 0.580 Chirality : 0.063 0.190 1068 Planarity : 0.005 0.017 984 Dihedral : 8.174 39.526 852 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.60 % Favored : 91.67 % Rotamer: Outliers : 0.33 % Allowed : 6.17 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.95 % 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: -2.97 (0.26), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.026 0.004 PHE E 94 TYR 0.031 0.005 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 SER cc_start: 0.8830 (t) cc_final: 0.8627 (t) REVERT: F 44 THR cc_start: 0.7628 (p) cc_final: 0.7413 (m) REVERT: F 92 THR cc_start: 0.7872 (p) cc_final: 0.7388 (p) REVERT: J 45 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7636 (mtpp) REVERT: M 45 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8267 (ttmt) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.2278 time to fit residues: 33.5685 Evaluate side-chains 84 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5976 Z= 0.233 Angle : 0.583 6.894 8052 Z= 0.327 Chirality : 0.054 0.134 1068 Planarity : 0.002 0.013 984 Dihedral : 5.386 19.205 852 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -2.97 (0.25), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.010 0.001 PHE B 94 TYR 0.006 0.001 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 45 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7269 (mttp) REVERT: L 45 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7318 (mttp) REVERT: M 80 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7118 (pttp) REVERT: N 44 THR cc_start: 0.7028 (t) cc_final: 0.6736 (m) REVERT: N 80 LYS cc_start: 0.4666 (pptt) cc_final: 0.3750 (pttp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1965 time to fit residues: 28.1403 Evaluate side-chains 79 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5976 Z= 0.432 Angle : 0.806 12.839 8052 Z= 0.448 Chirality : 0.056 0.145 1068 Planarity : 0.004 0.021 984 Dihedral : 6.723 26.122 852 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.51 (0.23), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 50 PHE 0.012 0.002 PHE A 94 TYR 0.021 0.003 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.668 Fit side-chains REVERT: F 83 GLU cc_start: 0.6721 (tp30) cc_final: 0.6295 (tp30) REVERT: I 62 GLN cc_start: 0.4166 (mt0) cc_final: 0.3425 (mt0) REVERT: J 45 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7597 (ttmm) REVERT: L 45 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7242 (mttp) REVERT: L 92 THR cc_start: 0.7856 (p) cc_final: 0.7655 (p) REVERT: M 46 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7930 (tm-30) REVERT: M 80 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7442 (pttp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1899 time to fit residues: 29.1665 Evaluate side-chains 91 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN F 79 GLN J 79 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.7806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5976 Z= 0.161 Angle : 0.592 8.976 8052 Z= 0.329 Chirality : 0.055 0.195 1068 Planarity : 0.002 0.012 984 Dihedral : 4.947 14.670 852 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.24), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.008 0.001 PHE B 94 TYR 0.004 0.001 TYR M 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.656 Fit side-chains REVERT: C 46 GLU cc_start: 0.8342 (tt0) cc_final: 0.8026 (tp30) REVERT: E 20 GLU cc_start: 0.7433 (mp0) cc_final: 0.7198 (mp0) REVERT: E 46 GLU cc_start: 0.8052 (tt0) cc_final: 0.7398 (tt0) REVERT: L 45 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7291 (mttp) REVERT: M 55 VAL cc_start: 0.6564 (t) cc_final: 0.6344 (t) REVERT: M 80 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7305 (pttp) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2152 time to fit residues: 31.0619 Evaluate side-chains 84 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 chunk 47 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 50.0000 overall best weight: 3.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.8039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5976 Z= 0.194 Angle : 0.573 8.121 8052 Z= 0.316 Chirality : 0.054 0.168 1068 Planarity : 0.002 0.011 984 Dihedral : 4.793 16.538 852 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.17 % Allowed : 1.67 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.25), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 50 PHE 0.006 0.001 PHE B 94 TYR 0.011 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.673 Fit side-chains REVERT: C 20 GLU cc_start: 0.7356 (mp0) cc_final: 0.7083 (mp0) REVERT: C 46 GLU cc_start: 0.8286 (tt0) cc_final: 0.7959 (tp30) REVERT: E 46 GLU cc_start: 0.8013 (tt0) cc_final: 0.6772 (tm-30) REVERT: L 45 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7324 (mttp) REVERT: M 80 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7252 (pttp) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1915 time to fit residues: 25.7310 Evaluate side-chains 81 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.6685 moved from start: 0.8495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5976 Z= 0.301 Angle : 0.668 8.267 8052 Z= 0.369 Chirality : 0.054 0.167 1068 Planarity : 0.003 0.013 984 Dihedral : 5.514 20.404 852 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -3.21 (0.24), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 50 PHE 0.009 0.002 PHE B 94 TYR 0.018 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.692 Fit side-chains REVERT: E 46 GLU cc_start: 0.8057 (tt0) cc_final: 0.7513 (tm-30) REVERT: L 45 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7215 (mttp) REVERT: M 80 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7372 (pttp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1767 time to fit residues: 23.0838 Evaluate side-chains 84 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 55 optimal weight: 40.0000 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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: 0.6635 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5976 Z= 0.195 Angle : 0.597 9.608 8052 Z= 0.326 Chirality : 0.054 0.163 1068 Planarity : 0.002 0.014 984 Dihedral : 5.021 17.012 852 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -3.13 (0.24), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.006 0.001 PHE B 94 TYR 0.015 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.658 Fit side-chains REVERT: C 46 GLU cc_start: 0.8295 (tt0) cc_final: 0.7708 (tp30) REVERT: E 46 GLU cc_start: 0.8073 (tt0) cc_final: 0.6458 (tm-30) REVERT: K 62 GLN cc_start: 0.5213 (pm20) cc_final: 0.4888 (pm20) REVERT: L 45 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7091 (mttp) REVERT: M 46 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7670 (tm-30) REVERT: M 80 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7305 (pttp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1899 time to fit residues: 24.6809 Evaluate side-chains 77 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 overall best weight: 4.1964 ------------------------------------------------------------------------------- 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: 0.6637 moved from start: 0.8655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5976 Z= 0.205 Angle : 0.590 8.950 8052 Z= 0.322 Chirality : 0.053 0.166 1068 Planarity : 0.002 0.013 984 Dihedral : 4.873 16.266 852 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -3.15 (0.24), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 PHE 0.006 0.001 PHE B 94 TYR 0.011 0.001 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8306 (tt0) cc_final: 0.7445 (tp30) REVERT: D 59 THR cc_start: 0.5639 (t) cc_final: 0.4930 (p) REVERT: E 46 GLU cc_start: 0.8071 (tt0) cc_final: 0.6402 (tm-30) REVERT: F 83 GLU cc_start: 0.6546 (tp30) cc_final: 0.6194 (tp30) REVERT: J 80 LYS cc_start: 0.8051 (mttt) cc_final: 0.7820 (mttm) REVERT: L 45 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7139 (mttp) REVERT: M 46 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7722 (tm-30) REVERT: M 80 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7296 (pttp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1832 time to fit residues: 24.5228 Evaluate side-chains 83 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 chunk 51 optimal weight: 0.0060 chunk 40 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 overall best weight: 7.2006 ------------------------------------------------------------------------------- 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: 0.6712 moved from start: 0.9025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5976 Z= 0.295 Angle : 0.679 8.845 8052 Z= 0.370 Chirality : 0.054 0.170 1068 Planarity : 0.003 0.014 984 Dihedral : 5.570 20.520 852 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -3.38 (0.23), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 50 PHE 0.008 0.002 PHE E 94 TYR 0.019 0.002 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: D 37 VAL cc_start: 0.8512 (t) cc_final: 0.8278 (p) REVERT: E 46 GLU cc_start: 0.8100 (tt0) cc_final: 0.7614 (tm-30) REVERT: F 83 GLU cc_start: 0.6531 (tp30) cc_final: 0.6200 (tp30) REVERT: I 55 VAL cc_start: 0.6676 (t) cc_final: 0.6449 (t) REVERT: K 62 GLN cc_start: 0.5533 (pm20) cc_final: 0.4547 (pm20) REVERT: L 45 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7249 (mttp) REVERT: M 46 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7769 (tm-30) REVERT: M 80 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7083 (pptt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2012 time to fit residues: 27.3782 Evaluate side-chains 84 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 overall best weight: 12.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.160408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.138119 restraints weight = 12147.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.139648 restraints weight = 9679.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.140675 restraints weight = 8197.408| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.9609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 5976 Z= 0.481 Angle : 0.870 9.416 8052 Z= 0.480 Chirality : 0.059 0.185 1068 Planarity : 0.004 0.018 984 Dihedral : 6.928 27.792 852 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -3.97 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 50 PHE 0.012 0.003 PHE E 94 TYR 0.026 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.83 seconds wall clock time: 24 minutes 55.80 seconds (1495.80 seconds total)