Starting phenix.real_space_refine on Thu Oct 22 23:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhx_49433/10_2026/9nhx_49433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhx_49433/10_2026/9nhx_49433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nhx_49433/10_2026/9nhx_49433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhx_49433/10_2026/9nhx_49433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nhx_49433/10_2026/9nhx_49433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhx_49433/10_2026/9nhx_49433.map" } resolution = 4.5 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= 0.024 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 S 6 5.16 5 C 4200 2.51 5 N 1212 2.21 5 O 1314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6732 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1122 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1122 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1122 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1122 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1122 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1122 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 1.56, per 1000 atoms: 0.23 Number of scatterers: 6732 At special positions: 0 Unit cell: (77.648, 80.18, 123.224, 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) S 6 16.00 O 1314 8.00 N 1212 7.00 C 4200 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: 0.50 Conformation dependent library (CDL) restraints added in 565.2 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 75.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.612A pdb=" N GLU A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.998A pdb=" N GLN A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 83 through 111 removed outlier: 4.472A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 137 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.612A pdb=" N GLU B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 55 removed outlier: 3.997A pdb=" N GLN B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 74 Processing helix chain 'B' and resid 83 through 111 removed outlier: 4.472A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 137 Processing helix chain 'B' and resid 155 through 164 Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.612A pdb=" N GLU C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 55 removed outlier: 3.997A pdb=" N GLN C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 74 Processing helix chain 'C' and resid 83 through 111 removed outlier: 4.472A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 137 Processing helix chain 'C' and resid 155 through 164 Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.612A pdb=" N GLU D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 55 removed outlier: 3.997A pdb=" N GLN D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 74 Processing helix chain 'D' and resid 83 through 111 removed outlier: 4.472A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 137 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.611A pdb=" N GLU E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 55 removed outlier: 3.998A pdb=" N GLN E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 74 Processing helix chain 'E' and resid 83 through 111 removed outlier: 4.471A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 137 Processing helix chain 'E' and resid 155 through 164 Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.612A pdb=" N GLU F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 55 removed outlier: 3.996A pdb=" N GLN F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 74 Processing helix chain 'F' and resid 83 through 111 removed outlier: 4.471A pdb=" N GLN F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 137 Processing helix chain 'F' and resid 155 through 164 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.925A pdb=" N GLY A 30 " --> pdb=" O LEU A 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.924A pdb=" N GLY B 30 " --> pdb=" O LEU B 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.924A pdb=" N GLY C 30 " --> pdb=" O LEU C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.924A pdb=" N GLY D 30 " --> pdb=" O LEU D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 29 through 31 removed outlier: 6.924A pdb=" N GLY E 30 " --> pdb=" O LEU E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 29 through 31 removed outlier: 6.925A pdb=" N GLY F 30 " --> pdb=" O LEU F 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 474 hydrogen bonds defined for protein. 1422 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: 0.97 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2358 1.34 - 1.46: 693 1.46 - 1.57: 3729 1.57 - 1.69: 6 1.69 - 1.80: 12 Bond restraints: 6798 Sorted by residual: bond pdb=" CB GLU D 54 " pdb=" CG GLU D 54 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.25e+00 bond pdb=" CB GLU A 54 " pdb=" CG GLU A 54 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.23e+00 bond pdb=" CB GLU B 54 " pdb=" CG GLU B 54 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.22e+00 bond pdb=" CB GLU E 54 " pdb=" CG GLU E 54 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.20e+00 bond pdb=" CB GLU C 54 " pdb=" CG GLU C 54 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.20e+00 ... (remaining 6793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 8936 2.69 - 5.39: 166 5.39 - 8.08: 18 8.08 - 10.77: 6 10.77 - 13.47: 6 Bond angle restraints: 9132 Sorted by residual: angle pdb=" CA GLU E 54 " pdb=" CB GLU E 54 " pdb=" CG GLU E 54 " ideal model delta sigma weight residual 114.10 127.57 -13.47 2.00e+00 2.50e-01 4.53e+01 angle pdb=" CA GLU A 54 " pdb=" CB GLU A 54 " pdb=" CG GLU A 54 " ideal model delta sigma weight residual 114.10 127.56 -13.46 2.00e+00 2.50e-01 4.53e+01 angle pdb=" CA GLU F 54 " pdb=" CB GLU F 54 " pdb=" CG GLU F 54 " ideal model delta sigma weight residual 114.10 127.54 -13.44 2.00e+00 2.50e-01 4.52e+01 angle pdb=" CA GLU C 54 " pdb=" CB GLU C 54 " pdb=" CG GLU C 54 " ideal model delta sigma weight residual 114.10 127.54 -13.44 2.00e+00 2.50e-01 4.51e+01 angle pdb=" CA GLU D 54 " pdb=" CB GLU D 54 " pdb=" CG GLU D 54 " ideal model delta sigma weight residual 114.10 127.52 -13.42 2.00e+00 2.50e-01 4.50e+01 ... (remaining 9127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 3348 14.94 - 29.88: 455 29.88 - 44.82: 270 44.82 - 59.76: 126 59.76 - 74.70: 19 Dihedral angle restraints: 4218 sinusoidal: 1734 harmonic: 2484 Sorted by residual: dihedral pdb=" CA GLU B 108 " pdb=" C GLU B 108 " pdb=" N GLU B 109 " pdb=" CA GLU B 109 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLU D 108 " pdb=" C GLU D 108 " pdb=" N GLU D 109 " pdb=" CA GLU D 109 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLU A 108 " pdb=" C GLU A 108 " pdb=" N GLU A 109 " pdb=" CA GLU A 109 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 4215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 573 0.031 - 0.061: 274 0.061 - 0.092: 100 0.092 - 0.122: 37 0.122 - 0.153: 24 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA GLU F 91 " pdb=" N GLU F 91 " pdb=" C GLU F 91 " pdb=" CB GLU F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA GLU C 91 " pdb=" N GLU C 91 " pdb=" C GLU C 91 " pdb=" CB GLU C 91 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA GLU D 91 " pdb=" N GLU D 91 " pdb=" C GLU D 91 " pdb=" CB GLU D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1005 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 111 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TYR F 111 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR F 111 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN F 112 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 111 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.13e+01 pdb=" C TYR C 111 " 0.058 2.00e-02 2.50e+03 pdb=" O TYR C 111 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 112 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 111 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C TYR E 111 " 0.058 2.00e-02 2.50e+03 pdb=" O TYR E 111 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN E 112 " -0.020 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 335 2.71 - 3.25: 7579 3.25 - 3.80: 11355 3.80 - 4.35: 14891 4.35 - 4.90: 22181 Nonbonded interactions: 56341 Sorted by model distance: nonbonded pdb=" O LYS B 49 " pdb=" OG SER B 53 " model vdw 2.158 3.040 nonbonded pdb=" O LYS C 49 " pdb=" OG SER C 53 " model vdw 2.158 3.040 nonbonded pdb=" O LYS F 49 " pdb=" OG SER F 53 " model vdw 2.159 3.040 nonbonded pdb=" O LYS E 49 " pdb=" OG SER E 53 " model vdw 2.159 3.040 nonbonded pdb=" O LYS A 49 " pdb=" OG SER A 53 " model vdw 2.159 3.040 ... (remaining 56336 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. 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: 2.340 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.004 0.062 6798 Z= 0.220 Angle : 0.986 13.466 9132 Z= 0.588 Chirality : 0.047 0.153 1008 Planarity : 0.006 0.034 1218 Dihedral : 20.652 74.700 2598 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.70 % Favored : 90.58 % Rotamer: Outliers : 14.04 % Allowed : 14.91 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.63 (0.23), residues: 828 helix: -3.88 (0.13), residues: 600 sheet: None (None), residues: 0 loop : -2.50 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 74 TYR 0.003 0.001 TYR A 148 PHE 0.013 0.002 PHE C 119 TRP 0.002 0.000 TRP C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.22 ( 6798) covalent geometry : angle 0.98551 / 0.59 ( 9132) hydrogen bonds : bond 0.15717 / 9.91 ( 474) hydrogen bonds : angle 9.16575 / 6.34 ( 1422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6691 (mmm160) REVERT: A 103 LYS cc_start: 0.8901 (mttt) cc_final: 0.8314 (tptp) REVERT: A 111 TYR cc_start: 0.8786 (m-10) cc_final: 0.8477 (m-80) outliers start: 16 outliers final: 6 residues processed: 53 average time/residue: 0.1038 time to fit residues: 5.7978 Evaluate side-chains 29 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.055042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.039064 restraints weight = 8348.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.040018 restraints weight = 6336.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.040767 restraints weight = 5185.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.041308 restraints weight = 4448.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.041819 restraints weight = 3905.291| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6798 Z= 0.189 Angle : 0.778 8.612 9132 Z= 0.419 Chirality : 0.049 0.161 1008 Planarity : 0.004 0.020 1218 Dihedral : 7.341 27.137 918 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % 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: -4.80 (0.22), residues: 828 helix: -3.05 (0.16), residues: 600 sheet: None (None), residues: 0 loop : -2.89 (0.31), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 101 TYR 0.009 0.001 TYR A 38 PHE 0.010 0.002 PHE C 100 TRP 0.007 0.002 TRP C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 ( 6798) covalent geometry : angle 0.77774 / 0.42 ( 9132) hydrogen bonds : bond 0.07335 / 4.89 ( 474) hydrogen bonds : angle 8.03382 / 5.57 ( 1422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 TYR cc_start: 0.9142 (m-10) cc_final: 0.8870 (m-10) REVERT: B 114 ARG cc_start: 0.9132 (tmm-80) cc_final: 0.8846 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1041 time to fit residues: 6.1459 Evaluate side-chains 22 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [61, 44, 30, 5, 39, 70, 9, 1, 58, 63, 56] chunk 61 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.080342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.067593 restraints weight = 10537.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.068981 restraints weight = 6598.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.069900 restraints weight = 4819.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.070405 restraints weight = 3920.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.070888 restraints weight = 3470.523| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.7811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6798 Z= 0.195 Angle : 0.832 8.565 9132 Z= 0.465 Chirality : 0.049 0.143 1008 Planarity : 0.005 0.043 1218 Dihedral : 6.877 22.291 918 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % 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: -3.71 (0.25), residues: 828 helix: -2.30 (0.17), residues: 618 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 101 TYR 0.006 0.001 TYR D 139 PHE 0.008 0.002 PHE C 100 TRP 0.000 0.000 TRP F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 ( 6798) covalent geometry : angle 0.83189 / 0.47 ( 9132) hydrogen bonds : bond 0.06600 / 4.50 ( 474) hydrogen bonds : angle 7.82437 / 5.44 ( 1422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 LEU cc_start: 0.9018 (tt) cc_final: 0.8753 (tt) REVERT: B 111 TYR cc_start: 0.9219 (m-10) cc_final: 0.8958 (m-10) REVERT: B 135 LYS cc_start: 0.9400 (pttm) cc_final: 0.9191 (mmmt) REVERT: B 164 ASN cc_start: 0.9187 (m-40) cc_final: 0.8876 (m110) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1080 time to fit residues: 4.9106 Evaluate side-chains 28 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [63, 29, 14, 49, 59, 65, 72, 79, 28, 51, 64] chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 79 optimal weight: 0.0770 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.054396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.041699 restraints weight = 9033.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.042616 restraints weight = 6763.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.043283 restraints weight = 5498.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.043775 restraints weight = 4695.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.044085 restraints weight = 4174.632| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.8666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6798 Z= 0.170 Angle : 0.786 8.410 9132 Z= 0.436 Chirality : 0.051 0.157 1008 Planarity : 0.004 0.019 1218 Dihedral : 6.599 20.316 918 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % 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 (0.27), residues: 828 helix: -1.81 (0.19), residues: 606 sheet: None (None), residues: 0 loop : -1.82 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 58 TYR 0.014 0.002 TYR E 38 PHE 0.010 0.002 PHE D 55 TRP 0.005 0.001 TRP F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 ( 6798) covalent geometry : angle 0.78598 / 0.44 ( 9132) hydrogen bonds : bond 0.05922 / 4.00 ( 474) hydrogen bonds : angle 7.34106 / 5.10 ( 1422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ILE cc_start: 0.9321 (mp) cc_final: 0.8827 (mp) REVERT: B 65 LEU cc_start: 0.8351 (mt) cc_final: 0.8145 (mt) REVERT: B 114 ARG cc_start: 0.9510 (mtm110) cc_final: 0.9125 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1007 time to fit residues: 4.5833 Evaluate side-chains 24 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [78, 67, 25, 35, 37, 20, 23, 75, 28, 17, 16] chunk 78 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 25 optimal weight: 0.0030 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 0.0170 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.055624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.039585 restraints weight = 8604.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.040743 restraints weight = 6240.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.041595 restraints weight = 4927.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.042190 restraints weight = 4125.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.042677 restraints weight = 3617.532| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.9684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6798 Z= 0.157 Angle : 0.795 8.743 9132 Z= 0.425 Chirality : 0.050 0.148 1008 Planarity : 0.004 0.017 1218 Dihedral : 6.186 18.740 918 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: -2.74 (0.28), residues: 828 helix: -1.59 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -1.93 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 94 TYR 0.015 0.002 TYR D 38 PHE 0.010 0.002 PHE D 100 TRP 0.007 0.001 TRP E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 6798) covalent geometry : angle 0.79492 / 0.42 ( 9132) hydrogen bonds : bond 0.05327 / 3.60 ( 474) hydrogen bonds : angle 6.79262 / 4.72 ( 1422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ILE cc_start: 0.8914 (mp) cc_final: 0.8470 (mp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1104 time to fit residues: 4.6431 Evaluate side-chains 28 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [3, 62, 60, 9, 73, 67, 6, 17, 80, 59, 72] chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 60 optimal weight: 0.0040 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 0.0170 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 chunk 80 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.080619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.066849 restraints weight = 10560.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.068326 restraints weight = 6777.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.069175 restraints weight = 5084.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.069728 restraints weight = 4242.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.069960 restraints weight = 3757.499| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 1.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6798 Z= 0.146 Angle : 0.760 7.587 9132 Z= 0.399 Chirality : 0.049 0.146 1008 Planarity : 0.004 0.021 1218 Dihedral : 6.016 18.662 918 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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 (0.27), residues: 828 helix: -1.41 (0.19), residues: 618 sheet: None (None), residues: 0 loop : -2.28 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 115 TYR 0.011 0.002 TYR F 139 PHE 0.010 0.002 PHE B 119 TRP 0.008 0.002 TRP E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 6798) covalent geometry : angle 0.76023 / 0.40 ( 9132) hydrogen bonds : bond 0.05046 / 3.41 ( 474) hydrogen bonds : angle 6.37810 / 4.45 ( 1422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ILE cc_start: 0.9340 (mp) cc_final: 0.8747 (mp) REVERT: B 111 TYR cc_start: 0.9009 (m-10) cc_final: 0.8786 (m-80) REVERT: B 114 ARG cc_start: 0.9485 (mtp-110) cc_final: 0.9035 (mtm110) REVERT: B 133 ILE cc_start: 0.9599 (tp) cc_final: 0.9103 (tp) REVERT: B 137 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8399 (mm-30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1171 time to fit residues: 4.7115 Evaluate side-chains 25 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [61, 39, 42, 1, 73, 77, 76, 37, 13, 43, 11] chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.0270 chunk 76 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.057581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.041695 restraints weight = 8497.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.042760 restraints weight = 6367.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.043573 restraints weight = 5186.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.044102 restraints weight = 4424.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.044612 restraints weight = 3942.598| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 1.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6798 Z= 0.160 Angle : 0.862 7.445 9132 Z= 0.469 Chirality : 0.052 0.177 1008 Planarity : 0.004 0.016 1218 Dihedral : 5.978 20.619 918 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.56 (0.27), residues: 828 helix: -1.32 (0.18), residues: 612 sheet: None (None), residues: 0 loop : -2.33 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 101 TYR 0.009 0.001 TYR F 111 PHE 0.008 0.001 PHE A 55 TRP 0.000 0.000 TRP F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 6798) covalent geometry : angle 0.86205 / 0.47 ( 9132) hydrogen bonds : bond 0.05072 / 3.42 ( 474) hydrogen bonds : angle 6.17513 / 4.29 ( 1422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ILE cc_start: 0.8827 (mp) cc_final: 0.8158 (tp) REVERT: B 114 ARG cc_start: 0.9487 (mtp-110) cc_final: 0.9284 (mtp180) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1247 time to fit residues: 4.9793 Evaluate side-chains 25 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [68, 37, 55, 75, 0, 83, 63, 8, 60, 59, 70] chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 75 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.080681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.065868 restraints weight = 10408.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.067358 restraints weight = 6756.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.068327 restraints weight = 5133.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.068874 restraints weight = 4289.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.068874 restraints weight = 3848.192| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 1.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6798 Z= 0.165 Angle : 0.827 7.393 9132 Z= 0.456 Chirality : 0.054 0.188 1008 Planarity : 0.004 0.028 1218 Dihedral : 5.844 18.041 918 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.28 (0.27), residues: 828 helix: -0.82 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -3.28 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 115 TYR 0.007 0.001 TYR B 148 PHE 0.026 0.003 PHE C 119 TRP 0.005 0.001 TRP C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 ( 6798) covalent geometry : angle 0.82746 / 0.46 ( 9132) hydrogen bonds : bond 0.04864 / 3.29 ( 474) hydrogen bonds : angle 6.12601 / 4.29 ( 1422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 TYR cc_start: 0.9403 (m-10) cc_final: 0.9182 (m-10) REVERT: B 114 ARG cc_start: 0.9392 (mtp-110) cc_final: 0.9112 (mtp-110) REVERT: B 118 GLU cc_start: 0.9517 (mp0) cc_final: 0.9271 (mp0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1253 time to fit residues: 4.8548 Evaluate side-chains 28 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [14, 26, 57, 37, 75, 38, 0, 78, 44, 34, 11] chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.0040 chunk 57 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.081541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.066794 restraints weight = 10421.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.068336 restraints weight = 6751.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.069172 restraints weight = 5108.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.069467 restraints weight = 4331.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.070059 restraints weight = 4003.057| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 1.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6798 Z= 0.163 Angle : 0.816 7.418 9132 Z= 0.451 Chirality : 0.054 0.201 1008 Planarity : 0.004 0.032 1218 Dihedral : 5.716 18.022 918 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: -2.10 (0.27), residues: 828 helix: -0.76 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -3.04 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 115 TYR 0.004 0.001 TYR E 153 PHE 0.033 0.003 PHE E 119 TRP 0.001 0.000 TRP B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 6798) covalent geometry : angle 0.81613 / 0.45 ( 9132) hydrogen bonds : bond 0.04717 / 3.17 ( 474) hydrogen bonds : angle 6.13623 / 4.30 ( 1422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 TYR cc_start: 0.9087 (m-10) cc_final: 0.8762 (m-10) REVERT: B 114 ARG cc_start: 0.9160 (mtp-110) cc_final: 0.8852 (mtp-110) REVERT: B 118 GLU cc_start: 0.9311 (mp0) cc_final: 0.9111 (mp0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1200 time to fit residues: 4.4240 Evaluate side-chains 28 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [50, 60, 71, 2, 34, 80, 51, 72, 14, 38, 47] chunk 50 optimal weight: 0.2980 chunk 60 optimal weight: 0.0870 chunk 71 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 47 optimal weight: 0.0670 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.058062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.041821 restraints weight = 8369.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.043025 restraints weight = 6116.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.043920 restraints weight = 4877.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.044557 restraints weight = 4128.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.045097 restraints weight = 3590.197| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 1.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6798 Z= 0.170 Angle : 0.849 7.973 9132 Z= 0.469 Chirality : 0.053 0.169 1008 Planarity : 0.004 0.038 1218 Dihedral : 5.519 17.744 918 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.80 (0.27), residues: 828 helix: -0.55 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -2.93 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 115 TYR 0.004 0.001 TYR C 148 PHE 0.024 0.002 PHE A 119 TRP 0.004 0.001 TRP E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 6798) covalent geometry : angle 0.84877 / 0.47 ( 9132) hydrogen bonds : bond 0.04727 / 3.14 ( 474) hydrogen bonds : angle 5.92569 / 4.13 ( 1422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1195 time to fit residues: 4.1346 Evaluate side-chains 26 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [72, 73, 64, 48, 21, 59, 5, 32, 47, 80, 39] chunk 72 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 5 optimal weight: 0.1980 chunk 32 optimal weight: 0.0980 chunk 47 optimal weight: 0.0020 chunk 80 optimal weight: 0.0870 chunk 39 optimal weight: 0.0170 overall best weight: 0.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.083605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.068540 restraints weight = 10308.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.069983 restraints weight = 6898.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.070959 restraints weight = 5334.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.071589 restraints weight = 4503.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.071916 restraints weight = 4025.014| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 1.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6798 Z= 0.164 Angle : 0.835 8.236 9132 Z= 0.462 Chirality : 0.055 0.184 1008 Planarity : 0.005 0.036 1218 Dihedral : 5.468 21.309 918 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.61 (0.27), residues: 828 helix: -0.41 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -2.87 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 115 TYR 0.006 0.001 TYR A 111 PHE 0.023 0.002 PHE F 119 TRP 0.001 0.000 TRP B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 6798) covalent geometry : angle 0.83455 / 0.46 ( 9132) hydrogen bonds : bond 0.04441 / 2.99 ( 474) hydrogen bonds : angle 5.75879 / 4.01 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 863.19 seconds wall clock time: 15 minutes 41.22 seconds (941.22 seconds total)