Starting phenix.real_space_refine on Wed Sep 17 04:38:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihc_52864/09_2025/9ihc_52864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihc_52864/09_2025/9ihc_52864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ihc_52864/09_2025/9ihc_52864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihc_52864/09_2025/9ihc_52864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ihc_52864/09_2025/9ihc_52864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihc_52864/09_2025/9ihc_52864.map" } resolution = 2.95 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= 0.005 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 13 5.16 5 C 2707 2.51 5 N 716 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4288 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 944 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1692 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "L" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Time building chain proxies: 1.38, per 1000 atoms: 0.32 Number of scatterers: 4288 At special positions: 0 Unit cell: (59.85, 62.13, 116.85, 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 13 16.00 O 852 8.00 N 716 7.00 C 2707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 235 " distance=2.03 Simple disulfide: pdb=" SG CYS H 255 " - pdb=" SG CYS L 240 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 160 " - pdb=" SG CYS L 220 " distance=2.03 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: 0.35 Conformation dependent library (CDL) restraints added in 195.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1046 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 13 sheets defined 7.1% alpha, 50.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 211 through 218 removed outlier: 3.860A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 57 removed outlier: 3.649A pdb=" N SER H 57 " --> pdb=" O ASN H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 57' Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.646A pdb=" N THR H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 226 through 228 No H-bonds generated for 'chain 'H' and resid 226 through 228' Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.803A pdb=" N PHE L 108 " --> pdb=" O PRO L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 209 through 214 Processing sheet with id=AA1, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.522A pdb=" N ALA B 205 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS B 241 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU B 207 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR B 243 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 209 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.712A pdb=" N GLN B 249 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 29 through 33 Processing sheet with id=AA4, first strand: chain 'H' and resid 36 through 38 removed outlier: 6.216A pdb=" N GLY H 36 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER H 59 " --> pdb=" O TYR H 125 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR H 83 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 36 through 38 removed outlier: 6.216A pdb=" N GLY H 36 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS H 122 " --> pdb=" O TRP H 142 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP H 142 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG H 124 " --> pdb=" O ASP H 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP H 140 " --> pdb=" O ARG H 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 163 removed outlier: 4.998A pdb=" N ALA H 176 " --> pdb=" O VAL H 223 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL H 223 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLY H 178 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL H 221 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU H 180 " --> pdb=" O SER H 219 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER H 219 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS H 182 " --> pdb=" O LEU H 217 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU H 217 " --> pdb=" O LYS H 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 159 through 163 removed outlier: 4.998A pdb=" N ALA H 176 " --> pdb=" O VAL H 223 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL H 223 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLY H 178 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL H 221 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU H 180 " --> pdb=" O SER H 219 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER H 219 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS H 182 " --> pdb=" O LEU H 217 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU H 217 " --> pdb=" O LYS H 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 190 through 193 removed outlier: 4.263A pdb=" N TYR H 233 " --> pdb=" O VAL H 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 29 through 32 Processing sheet with id=AB1, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.576A pdb=" N LEU L 36 " --> pdb=" O GLU L 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL L 58 " --> pdb=" O TYR L 74 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR L 74 " --> pdb=" O VAL L 58 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 60 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.576A pdb=" N LEU L 36 " --> pdb=" O GLU L 131 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR L 123 " --> pdb=" O GLN L 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 140 through 144 removed outlier: 5.780A pdb=" N TYR L 199 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 171 through 176 177 hydrogen bonds defined for protein. 441 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: 0.68 Time building geometry restraints manager: 0.48 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: 1358 1.34 - 1.46: 1045 1.46 - 1.58: 1971 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 4390 Sorted by residual: bond pdb=" N ASP L 26 " pdb=" CA ASP L 26 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.57e+00 bond pdb=" N GLN L 115 " pdb=" CA GLN L 115 " ideal model delta sigma weight residual 1.456 1.480 -0.024 1.25e-02 6.40e+03 3.62e+00 bond pdb=" N SER L 25 " pdb=" CA SER L 25 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.31e+00 bond pdb=" C GLN L 115 " pdb=" O GLN L 115 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.21e-02 6.83e+03 2.05e+00 bond pdb=" CB GLN H 231 " pdb=" CG GLN H 231 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 ... (remaining 4385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 5778 1.37 - 2.74: 155 2.74 - 4.12: 29 4.12 - 5.49: 10 5.49 - 6.86: 2 Bond angle restraints: 5974 Sorted by residual: angle pdb=" CA GLN H 231 " pdb=" CB GLN H 231 " pdb=" CG GLN H 231 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C SER L 75 " pdb=" N ALA L 76 " pdb=" CA ALA L 76 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.59e+00 angle pdb=" CB GLN H 231 " pdb=" CG GLN H 231 " pdb=" CD GLN H 231 " ideal model delta sigma weight residual 112.60 117.75 -5.15 1.70e+00 3.46e-01 9.19e+00 angle pdb=" C GLN L 115 " pdb=" CA GLN L 115 " pdb=" CB GLN L 115 " ideal model delta sigma weight residual 109.84 114.58 -4.74 1.63e+00 3.76e-01 8.47e+00 angle pdb=" CA GLU L 169 " pdb=" CB GLU L 169 " pdb=" CG GLU L 169 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.73e+00 ... (remaining 5969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 2332 16.87 - 33.75: 193 33.75 - 50.62: 62 50.62 - 67.50: 17 67.50 - 84.37: 5 Dihedral angle restraints: 2609 sinusoidal: 974 harmonic: 1635 Sorted by residual: dihedral pdb=" CB CYS H 255 " pdb=" SG CYS H 255 " pdb=" SG CYS L 240 " pdb=" CB CYS L 240 " ideal model delta sinusoidal sigma weight residual -86.00 -134.81 48.81 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS L 48 " pdb=" SG CYS L 48 " pdb=" SG CYS L 113 " pdb=" CB CYS L 113 " ideal model delta sinusoidal sigma weight residual 93.00 124.01 -31.01 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CB CYS H 48 " pdb=" SG CYS H 48 " pdb=" SG CYS H 122 " pdb=" CB CYS H 122 " ideal model delta sinusoidal sigma weight residual 93.00 66.71 26.29 1 1.00e+01 1.00e-02 9.93e+00 ... (remaining 2606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 363 0.028 - 0.056: 200 0.056 - 0.084: 50 0.084 - 0.112: 41 0.112 - 0.140: 15 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA VAL H 221 " pdb=" N VAL H 221 " pdb=" C VAL H 221 " pdb=" CB VAL H 221 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE B 314 " pdb=" N ILE B 314 " pdb=" C ILE B 314 " pdb=" CB ILE B 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL H 63 " pdb=" N VAL H 63 " pdb=" C VAL H 63 " pdb=" CB VAL H 63 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 666 not shown) Planarity restraints: 758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 286 " -0.009 2.00e-02 2.50e+03 1.16e-02 2.71e+00 pdb=" CG TYR B 286 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 286 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 286 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 286 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 286 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 83 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO L 84 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 104 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO L 105 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO L 105 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 105 " 0.018 5.00e-02 4.00e+02 ... (remaining 755 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1513 2.86 - 3.37: 3497 3.37 - 3.88: 7355 3.88 - 4.39: 8114 4.39 - 4.90: 14514 Nonbonded interactions: 34993 Sorted by model distance: nonbonded pdb=" O GLN B 236 " pdb=" OH TYR B 312 " model vdw 2.349 3.040 nonbonded pdb=" N GLU L 106 " pdb=" OE1 GLU L 106 " model vdw 2.363 3.120 nonbonded pdb=" ND2 ASN H 130 " pdb=" OG SER L 56 " model vdw 2.364 3.120 nonbonded pdb=" O ASP L 107 " pdb=" OH TYR L 111 " model vdw 2.365 3.040 nonbonded pdb=" N ASP L 196 " pdb=" OD1 ASP L 196 " model vdw 2.374 3.120 ... (remaining 34988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.620 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: 0.010 Set scattering table: 0.010 Process input model: 6.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 0.041 4395 Z= 0.156 Angle : 0.583 6.862 5984 Z= 0.324 Chirality : 0.044 0.140 669 Planarity : 0.005 0.033 758 Dihedral : 14.943 84.372 1548 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.62 % Allowed : 15.59 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 0.55 (0.35), residues: 552 helix: -1.81 (0.84), residues: 22 sheet: 0.51 (0.30), residues: 289 loop : 0.61 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 237 TYR 0.029 0.002 TYR B 286 PHE 0.011 0.001 PHE B 261 TRP 0.008 0.001 TRP H 142 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4390) covalent geometry : angle 0.58363 ( 5974) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.30086 ( 10) hydrogen bonds : bond 0.06895 ( 163) hydrogen bonds : angle 6.43158 ( 441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9255 (ptmm) cc_final: 0.8986 (ptpt) REVERT: B 301 LYS cc_start: 0.8302 (mmmm) cc_final: 0.8008 (mmmm) REVERT: B 317 GLN cc_start: 0.7866 (tt0) cc_final: 0.7372 (mt0) REVERT: B 318 LYS cc_start: 0.9033 (tttt) cc_final: 0.8595 (tttm) REVERT: H 238 ASN cc_start: 0.8422 (t0) cc_final: 0.8137 (t0) REVERT: L 168 ARG cc_start: 0.8447 (ptm160) cc_final: 0.8094 (tmt90) REVERT: L 169 GLU cc_start: 0.8341 (pp20) cc_final: 0.8111 (pp20) outliers start: 3 outliers final: 3 residues processed: 81 average time/residue: 0.6392 time to fit residues: 53.4667 Evaluate side-chains 55 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 135 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.091795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073297 restraints weight = 8607.454| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.19 r_work: 0.2995 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4395 Z= 0.165 Angle : 0.488 4.468 5984 Z= 0.263 Chirality : 0.042 0.137 669 Planarity : 0.004 0.030 758 Dihedral : 4.750 46.877 607 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.70 % Allowed : 16.42 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 0.73 (0.36), residues: 552 helix: -1.64 (0.91), residues: 22 sheet: 0.68 (0.32), residues: 264 loop : 0.65 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 227 TYR 0.016 0.001 TYR B 286 PHE 0.009 0.001 PHE L 165 TRP 0.008 0.001 TRP H 142 HIS 0.002 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4390) covalent geometry : angle 0.48802 ( 5974) SS BOND : bond 0.00119 ( 5) SS BOND : angle 0.44412 ( 10) hydrogen bonds : bond 0.02781 ( 163) hydrogen bonds : angle 5.42524 ( 441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.181 Fit side-chains REVERT: B 257 LYS cc_start: 0.9158 (ptmm) cc_final: 0.8809 (ptpt) REVERT: B 260 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: B 275 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 310 TYR cc_start: 0.8456 (m-10) cc_final: 0.8137 (m-10) REVERT: B 317 GLN cc_start: 0.7650 (tt0) cc_final: 0.7126 (mt0) REVERT: B 318 LYS cc_start: 0.9017 (tttt) cc_final: 0.8598 (tttm) REVERT: H 238 ASN cc_start: 0.8409 (t0) cc_final: 0.8152 (t0) REVERT: L 168 ARG cc_start: 0.8434 (ptm160) cc_final: 0.8062 (tmt90) REVERT: L 169 GLU cc_start: 0.8223 (pp20) cc_final: 0.7943 (pp20) outliers start: 13 outliers final: 7 residues processed: 65 average time/residue: 0.6410 time to fit residues: 43.0848 Evaluate side-chains 57 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 48 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.071495 restraints weight = 8724.075| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.23 r_work: 0.2962 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 4395 Z= 0.204 Angle : 0.503 4.317 5984 Z= 0.271 Chirality : 0.043 0.139 669 Planarity : 0.004 0.035 758 Dihedral : 4.693 45.198 605 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.16 % Allowed : 15.38 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 0.70 (0.36), residues: 552 helix: -1.32 (0.96), residues: 22 sheet: 0.56 (0.32), residues: 264 loop : 0.72 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 227 TYR 0.020 0.001 TYR B 286 PHE 0.010 0.001 PHE L 165 TRP 0.010 0.001 TRP H 142 HIS 0.002 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4390) covalent geometry : angle 0.50262 ( 5974) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.58058 ( 10) hydrogen bonds : bond 0.02855 ( 163) hydrogen bonds : angle 5.48621 ( 441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9080 (ptmm) cc_final: 0.8692 (ptpt) REVERT: B 260 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: B 275 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 286 TYR cc_start: 0.9060 (p90) cc_final: 0.8855 (p90) REVERT: B 310 TYR cc_start: 0.8515 (m-10) cc_final: 0.8231 (m-10) REVERT: B 317 GLN cc_start: 0.7630 (tt0) cc_final: 0.7085 (mt0) REVERT: B 318 LYS cc_start: 0.9010 (tttt) cc_final: 0.8553 (tttm) REVERT: L 168 ARG cc_start: 0.8441 (ptm160) cc_final: 0.8067 (tmt90) REVERT: L 169 GLU cc_start: 0.8209 (pp20) cc_final: 0.7878 (pp20) REVERT: L 196 ASP cc_start: 0.8376 (p0) cc_final: 0.8176 (p0) outliers start: 20 outliers final: 8 residues processed: 68 average time/residue: 0.6083 time to fit residues: 42.8048 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 48 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.091651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073293 restraints weight = 8538.451| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.20 r_work: 0.3000 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4395 Z= 0.122 Angle : 0.470 4.414 5984 Z= 0.252 Chirality : 0.042 0.135 669 Planarity : 0.003 0.032 758 Dihedral : 4.448 45.492 605 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.95 % Allowed : 16.84 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 0.83 (0.37), residues: 552 helix: -1.26 (0.97), residues: 22 sheet: 0.56 (0.32), residues: 266 loop : 0.93 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 227 TYR 0.015 0.001 TYR B 286 PHE 0.009 0.001 PHE B 261 TRP 0.007 0.001 TRP H 142 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4390) covalent geometry : angle 0.47042 ( 5974) SS BOND : bond 0.00108 ( 5) SS BOND : angle 0.45757 ( 10) hydrogen bonds : bond 0.02561 ( 163) hydrogen bonds : angle 5.14880 ( 441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9098 (ptmm) cc_final: 0.8740 (ptpt) REVERT: B 260 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: B 275 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 276 GLN cc_start: 0.8763 (tt0) cc_final: 0.8366 (tt0) REVERT: B 286 TYR cc_start: 0.9020 (p90) cc_final: 0.8797 (p90) REVERT: B 310 TYR cc_start: 0.8501 (m-10) cc_final: 0.8212 (m-10) REVERT: B 317 GLN cc_start: 0.7630 (tt0) cc_final: 0.7091 (mt0) REVERT: B 318 LYS cc_start: 0.8975 (tttt) cc_final: 0.8530 (tttm) REVERT: L 168 ARG cc_start: 0.8445 (ptm160) cc_final: 0.8071 (tmt90) REVERT: L 169 GLU cc_start: 0.8167 (pp20) cc_final: 0.7796 (pp20) REVERT: L 196 ASP cc_start: 0.8322 (p0) cc_final: 0.8121 (p0) outliers start: 19 outliers final: 8 residues processed: 67 average time/residue: 0.5840 time to fit residues: 40.5502 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 213 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.091299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.073001 restraints weight = 8604.964| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.19 r_work: 0.2988 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4395 Z= 0.146 Angle : 0.492 7.521 5984 Z= 0.259 Chirality : 0.042 0.136 669 Planarity : 0.003 0.038 758 Dihedral : 4.433 44.493 605 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.95 % Allowed : 17.46 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 0.91 (0.37), residues: 552 helix: -0.95 (1.00), residues: 22 sheet: 0.56 (0.32), residues: 266 loop : 1.01 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 227 TYR 0.014 0.001 TYR B 286 PHE 0.009 0.001 PHE L 165 TRP 0.010 0.001 TRP L 174 HIS 0.002 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4390) covalent geometry : angle 0.49162 ( 5974) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.53442 ( 10) hydrogen bonds : bond 0.02560 ( 163) hydrogen bonds : angle 5.12900 ( 441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8661 (ptpt) REVERT: B 260 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: B 275 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7862 (tm-30) REVERT: B 276 GLN cc_start: 0.8768 (tt0) cc_final: 0.8357 (tt0) REVERT: B 286 TYR cc_start: 0.9023 (p90) cc_final: 0.8806 (p90) REVERT: B 310 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: B 317 GLN cc_start: 0.7632 (tt0) cc_final: 0.7102 (mt0) REVERT: B 318 LYS cc_start: 0.8962 (tttt) cc_final: 0.8507 (tttm) REVERT: H 231 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8729 (tp40) REVERT: L 168 ARG cc_start: 0.8435 (ptm160) cc_final: 0.8061 (tmt90) REVERT: L 169 GLU cc_start: 0.8147 (pp20) cc_final: 0.7762 (pp20) outliers start: 19 outliers final: 9 residues processed: 64 average time/residue: 0.6576 time to fit residues: 43.4866 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 231 GLN Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 213 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN L 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.076805 restraints weight = 8688.312| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.28 r_work: 0.3034 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4395 Z= 0.088 Angle : 0.465 6.786 5984 Z= 0.246 Chirality : 0.041 0.129 669 Planarity : 0.004 0.042 758 Dihedral : 4.245 45.320 605 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.33 % Allowed : 18.71 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 1.18 (0.37), residues: 552 helix: -1.14 (0.99), residues: 23 sheet: 0.80 (0.32), residues: 265 loop : 1.17 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 227 TYR 0.012 0.001 TYR B 286 PHE 0.008 0.001 PHE B 261 TRP 0.008 0.001 TRP L 174 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 4390) covalent geometry : angle 0.46458 ( 5974) SS BOND : bond 0.00133 ( 5) SS BOND : angle 0.43987 ( 10) hydrogen bonds : bond 0.02364 ( 163) hydrogen bonds : angle 4.75017 ( 441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.179 Fit side-chains REVERT: B 257 LYS cc_start: 0.9063 (ptmm) cc_final: 0.8698 (ptpt) REVERT: B 260 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: B 275 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 276 GLN cc_start: 0.8675 (tt0) cc_final: 0.8368 (tt0) REVERT: B 286 TYR cc_start: 0.8983 (p90) cc_final: 0.8773 (p90) REVERT: B 310 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8184 (m-10) REVERT: B 317 GLN cc_start: 0.7611 (tt0) cc_final: 0.7112 (mt0) REVERT: B 318 LYS cc_start: 0.8922 (tttt) cc_final: 0.8431 (tttm) REVERT: L 106 GLU cc_start: 0.8611 (pm20) cc_final: 0.8252 (pm20) REVERT: L 169 GLU cc_start: 0.8125 (pp20) cc_final: 0.7889 (pp20) REVERT: L 213 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8455 (mp0) outliers start: 16 outliers final: 5 residues processed: 65 average time/residue: 0.5877 time to fit residues: 39.6520 Evaluate side-chains 59 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 213 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 210 GLN L 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074653 restraints weight = 8793.055| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.26 r_work: 0.2987 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4395 Z= 0.141 Angle : 0.494 6.570 5984 Z= 0.261 Chirality : 0.042 0.135 669 Planarity : 0.004 0.047 758 Dihedral : 3.949 14.331 604 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.12 % Allowed : 19.54 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 1.13 (0.37), residues: 552 helix: -0.94 (1.02), residues: 23 sheet: 0.70 (0.32), residues: 266 loop : 1.20 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 227 TYR 0.012 0.001 TYR B 286 PHE 0.031 0.001 PHE B 261 TRP 0.008 0.001 TRP H 142 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4390) covalent geometry : angle 0.49415 ( 5974) SS BOND : bond 0.00096 ( 5) SS BOND : angle 0.57937 ( 10) hydrogen bonds : bond 0.02549 ( 163) hydrogen bonds : angle 4.88584 ( 441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8943 (ptmm) cc_final: 0.8543 (ptpt) REVERT: B 260 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: B 275 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 276 GLN cc_start: 0.8714 (tt0) cc_final: 0.8365 (tt0) REVERT: B 310 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.8214 (m-10) REVERT: B 317 GLN cc_start: 0.7620 (tt0) cc_final: 0.7101 (mt0) REVERT: B 318 LYS cc_start: 0.8937 (tttt) cc_final: 0.8589 (tttt) REVERT: H 231 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8621 (tp-100) REVERT: L 106 GLU cc_start: 0.8669 (pm20) cc_final: 0.8285 (pm20) REVERT: L 169 GLU cc_start: 0.8119 (pp20) cc_final: 0.7881 (pp20) outliers start: 15 outliers final: 9 residues processed: 63 average time/residue: 0.6366 time to fit residues: 41.5769 Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 213 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.0060 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077616 restraints weight = 8674.652| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.27 r_work: 0.3017 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4395 Z= 0.106 Angle : 0.489 6.280 5984 Z= 0.257 Chirality : 0.042 0.132 669 Planarity : 0.004 0.050 758 Dihedral : 3.889 14.173 604 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.29 % Allowed : 20.58 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 1.21 (0.37), residues: 552 helix: -1.03 (1.01), residues: 23 sheet: 0.75 (0.32), residues: 266 loop : 1.26 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 227 TYR 0.022 0.001 TYR B 286 PHE 0.030 0.001 PHE B 261 TRP 0.007 0.001 TRP H 193 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4390) covalent geometry : angle 0.48862 ( 5974) SS BOND : bond 0.00108 ( 5) SS BOND : angle 0.45222 ( 10) hydrogen bonds : bond 0.02389 ( 163) hydrogen bonds : angle 4.74905 ( 441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.182 Fit side-chains REVERT: B 257 LYS cc_start: 0.9007 (ptmm) cc_final: 0.8602 (ptpt) REVERT: B 260 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: B 275 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 276 GLN cc_start: 0.8716 (tt0) cc_final: 0.8425 (tt0) REVERT: B 310 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.8205 (m-10) REVERT: B 317 GLN cc_start: 0.7645 (tt0) cc_final: 0.7140 (mt0) REVERT: B 318 LYS cc_start: 0.8933 (tttt) cc_final: 0.8422 (tttm) REVERT: H 231 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8719 (tp-100) REVERT: L 106 GLU cc_start: 0.8658 (pm20) cc_final: 0.8292 (pm20) REVERT: L 169 GLU cc_start: 0.8123 (pp20) cc_final: 0.7911 (pp20) REVERT: L 213 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8430 (mp0) outliers start: 11 outliers final: 6 residues processed: 58 average time/residue: 0.6367 time to fit residues: 38.2175 Evaluate side-chains 59 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 213 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 overall best weight: 0.9158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.090820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072569 restraints weight = 8760.968| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.18 r_work: 0.2987 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4395 Z= 0.159 Angle : 0.515 6.114 5984 Z= 0.272 Chirality : 0.042 0.134 669 Planarity : 0.004 0.054 758 Dihedral : 4.098 14.878 604 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.08 % Allowed : 20.79 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 1.12 (0.37), residues: 552 helix: -0.84 (1.04), residues: 23 sheet: 0.67 (0.32), residues: 266 loop : 1.21 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 227 TYR 0.012 0.001 TYR H 121 PHE 0.031 0.001 PHE B 261 TRP 0.008 0.001 TRP H 142 HIS 0.002 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4390) covalent geometry : angle 0.51488 ( 5974) SS BOND : bond 0.00114 ( 5) SS BOND : angle 0.57112 ( 10) hydrogen bonds : bond 0.02618 ( 163) hydrogen bonds : angle 4.97635 ( 441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8960 (ptmm) cc_final: 0.8563 (ptpt) REVERT: B 260 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: B 275 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 276 GLN cc_start: 0.8741 (tt0) cc_final: 0.8392 (tt0) REVERT: B 301 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7549 (mppt) REVERT: B 310 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: B 317 GLN cc_start: 0.7653 (tt0) cc_final: 0.7140 (mt0) REVERT: B 318 LYS cc_start: 0.8942 (tttt) cc_final: 0.8466 (tttm) REVERT: L 106 GLU cc_start: 0.8696 (pm20) cc_final: 0.8285 (pm20) REVERT: L 169 GLU cc_start: 0.8152 (pp20) cc_final: 0.7935 (pp20) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.6676 time to fit residues: 39.3632 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072470 restraints weight = 8749.128| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.19 r_work: 0.2983 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4395 Z= 0.158 Angle : 0.519 6.117 5984 Z= 0.274 Chirality : 0.042 0.134 669 Planarity : 0.004 0.055 758 Dihedral : 4.133 14.637 604 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.49 % Allowed : 20.58 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 1.06 (0.37), residues: 552 helix: -0.87 (1.03), residues: 23 sheet: 0.61 (0.31), residues: 278 loop : 1.24 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 227 TYR 0.021 0.001 TYR B 286 PHE 0.031 0.001 PHE B 261 TRP 0.008 0.001 TRP H 142 HIS 0.002 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4390) covalent geometry : angle 0.51931 ( 5974) SS BOND : bond 0.00108 ( 5) SS BOND : angle 0.55684 ( 10) hydrogen bonds : bond 0.02614 ( 163) hydrogen bonds : angle 5.01078 ( 441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8968 (ptmm) cc_final: 0.8562 (ptpt) REVERT: B 260 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: B 301 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7533 (mppt) REVERT: B 310 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: B 317 GLN cc_start: 0.7646 (tt0) cc_final: 0.7089 (mt0) REVERT: B 318 LYS cc_start: 0.8943 (tttt) cc_final: 0.8590 (tttt) REVERT: L 106 GLU cc_start: 0.8689 (pm20) cc_final: 0.8291 (pm20) REVERT: L 169 GLU cc_start: 0.8145 (pp20) cc_final: 0.7848 (pp20) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 0.6472 time to fit residues: 40.8409 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 0.0370 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076424 restraints weight = 8729.481| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.28 r_work: 0.3028 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4395 Z= 0.102 Angle : 0.501 6.516 5984 Z= 0.264 Chirality : 0.042 0.131 669 Planarity : 0.004 0.054 758 Dihedral : 3.937 14.057 604 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.08 % Allowed : 21.21 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: 1.24 (0.38), residues: 552 helix: -0.97 (1.02), residues: 23 sheet: 0.76 (0.33), residues: 266 loop : 1.29 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 227 TYR 0.008 0.001 TYR H 121 PHE 0.029 0.001 PHE B 261 TRP 0.007 0.001 TRP H 193 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4390) covalent geometry : angle 0.50119 ( 5974) SS BOND : bond 0.00165 ( 5) SS BOND : angle 0.41520 ( 10) hydrogen bonds : bond 0.02434 ( 163) hydrogen bonds : angle 4.72503 ( 441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1669.95 seconds wall clock time: 29 minutes 23.95 seconds (1763.95 seconds total)