Starting phenix.real_space_refine on Sat May 10 00:13:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihc_52864/05_2025/9ihc_52864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihc_52864/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ihc_52864/05_2025/9ihc_52864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihc_52864/05_2025/9ihc_52864.map" model { file = "/net/cci-nas-00/data/ceres_data/9ihc_52864/05_2025/9ihc_52864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihc_52864/05_2025/9ihc_52864.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.62, per 1000 atoms: 0.84 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: 0.90 Conformation dependent library (CDL) restraints added in 490.7 milliseconds 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: 0.61 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: 1.24 Time building geometry restraints manager: 1.08 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: 3.890 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.050 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (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 TRP 0.008 0.001 TRP H 142 HIS 0.003 0.001 HIS B 285 PHE 0.011 0.001 PHE B 261 TYR 0.029 0.002 TYR B 286 ARG 0.007 0.001 ARG L 237 Details of bonding type rmsd hydrogen bonds : bond 0.06895 ( 163) hydrogen bonds : angle 6.43158 ( 441) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.30086 ( 10) covalent geometry : bond 0.00331 ( 4390) covalent geometry : angle 0.58363 ( 5974) *********************** 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 : 0.482 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: 1.2764 time to fit residues: 106.9483 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 : 0.525 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 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 = 0.3414 r_free = 0.3414 target = 0.088942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.070430 restraints weight = 8687.420| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.22 r_work: 0.2937 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.007 0.111 4395 Z= 0.281 Angle : 0.557 4.398 5984 Z= 0.299 Chirality : 0.044 0.139 669 Planarity : 0.004 0.032 758 Dihedral : 5.095 45.709 607 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.74 % Allowed : 14.97 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.35), residues: 552 helix: -1.51 (0.93), residues: 22 sheet: 0.50 (0.31), residues: 264 loop : 0.49 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 142 HIS 0.004 0.001 HIS H 133 PHE 0.010 0.001 PHE L 165 TYR 0.017 0.002 TYR B 286 ARG 0.007 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 163) hydrogen bonds : angle 5.82332 ( 441) SS BOND : bond 0.00284 ( 5) SS BOND : angle 0.65468 ( 10) covalent geometry : bond 0.00659 ( 4390) covalent geometry : angle 0.55687 ( 5974) *********************** 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 77 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9109 (ptmm) cc_final: 0.8748 (ptpt) REVERT: B 260 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: B 275 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8001 (tm-30) REVERT: B 310 TYR cc_start: 0.8503 (m-10) cc_final: 0.8180 (m-10) REVERT: B 318 LYS cc_start: 0.9023 (tttt) cc_final: 0.8627 (tttm) REVERT: L 168 ARG cc_start: 0.8450 (ptm160) cc_final: 0.8080 (tmt90) REVERT: L 169 GLU cc_start: 0.8233 (pp20) cc_final: 0.7955 (pp20) REVERT: L 196 ASP cc_start: 0.8367 (p0) cc_final: 0.8148 (p0) outliers start: 18 outliers final: 9 residues processed: 71 average time/residue: 1.1377 time to fit residues: 84.0344 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 H residue 255 CYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.090532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072024 restraints weight = 8548.864| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.20 r_work: 0.2973 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1470 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= 0.165 Angle : 0.488 4.263 5984 Z= 0.263 Chirality : 0.042 0.139 669 Planarity : 0.004 0.035 758 Dihedral : 4.737 45.582 606 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.95 % Allowed : 16.63 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.36), residues: 552 helix: -1.29 (0.95), residues: 22 sheet: 0.47 (0.32), residues: 264 loop : 0.72 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 142 HIS 0.002 0.001 HIS H 133 PHE 0.011 0.001 PHE L 165 TYR 0.019 0.001 TYR B 286 ARG 0.008 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 163) hydrogen bonds : angle 5.41146 ( 441) SS BOND : bond 0.00103 ( 5) SS BOND : angle 0.50731 ( 10) covalent geometry : bond 0.00385 ( 4390) covalent geometry : angle 0.48773 ( 5974) *********************** 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 77 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9085 (ptmm) cc_final: 0.8697 (ptpt) REVERT: B 260 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: B 275 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 276 GLN cc_start: 0.8727 (tt0) cc_final: 0.8330 (tt0) REVERT: B 310 TYR cc_start: 0.8509 (m-10) cc_final: 0.8231 (m-10) REVERT: B 317 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7123 (mt0) REVERT: B 318 LYS cc_start: 0.9006 (tttt) cc_final: 0.8557 (tttm) REVERT: H 231 GLN cc_start: 0.8739 (tp40) cc_final: 0.8514 (tp40) REVERT: H 238 ASN cc_start: 0.8387 (t0) cc_final: 0.8153 (t0) REVERT: L 168 ARG cc_start: 0.8441 (ptm160) cc_final: 0.8070 (tmt90) REVERT: L 169 GLU cc_start: 0.8196 (pp20) cc_final: 0.7859 (pp20) outliers start: 19 outliers final: 9 residues processed: 70 average time/residue: 1.2420 time to fit residues: 90.1754 Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 B residue 317 GLN 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 143 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.089580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071188 restraints weight = 8667.103| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.22 r_work: 0.2955 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4395 Z= 0.186 Angle : 0.495 4.267 5984 Z= 0.265 Chirality : 0.042 0.137 669 Planarity : 0.004 0.037 758 Dihedral : 4.620 43.790 605 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.78 % Allowed : 16.84 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.36), residues: 552 helix: -0.92 (0.99), residues: 22 sheet: 0.54 (0.32), residues: 261 loop : 0.74 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 142 HIS 0.003 0.001 HIS H 133 PHE 0.010 0.001 PHE L 165 TYR 0.012 0.001 TYR H 121 ARG 0.008 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02751 ( 163) hydrogen bonds : angle 5.39024 ( 441) SS BOND : bond 0.00155 ( 5) SS BOND : angle 0.59772 ( 10) covalent geometry : bond 0.00434 ( 4390) covalent geometry : angle 0.49431 ( 5974) *********************** 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 76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.531 Fit side-chains REVERT: B 257 LYS cc_start: 0.9047 (ptmm) cc_final: 0.8666 (ptpt) REVERT: B 260 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: B 275 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 276 GLN cc_start: 0.8756 (tt0) cc_final: 0.8301 (tt0) REVERT: B 310 TYR cc_start: 0.8525 (m-10) cc_final: 0.8235 (m-10) REVERT: B 317 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: B 318 LYS cc_start: 0.8978 (tttt) cc_final: 0.8649 (tttt) REVERT: L 106 GLU cc_start: 0.8662 (pm20) cc_final: 0.8245 (pm20) REVERT: L 168 ARG cc_start: 0.8453 (ptm160) cc_final: 0.8079 (tmt90) REVERT: L 169 GLU cc_start: 0.8201 (pp20) cc_final: 0.7838 (pp20) outliers start: 23 outliers final: 10 residues processed: 69 average time/residue: 1.0776 time to fit residues: 77.4603 Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 317 GLN 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 143 ILE Chi-restraints excluded: chain L residue 190 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.089244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070790 restraints weight = 8819.843| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.24 r_work: 0.2948 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 4395 Z= 0.201 Angle : 0.507 4.294 5984 Z= 0.272 Chirality : 0.043 0.138 669 Planarity : 0.004 0.038 758 Dihedral : 4.671 43.309 605 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.74 % Allowed : 18.71 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.36), residues: 552 helix: -0.73 (1.01), residues: 22 sheet: 0.50 (0.32), residues: 260 loop : 0.76 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 174 HIS 0.003 0.001 HIS H 133 PHE 0.010 0.001 PHE L 165 TYR 0.018 0.001 TYR B 286 ARG 0.009 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 163) hydrogen bonds : angle 5.41695 ( 441) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.59058 ( 10) covalent geometry : bond 0.00470 ( 4390) covalent geometry : angle 0.50681 ( 5974) *********************** 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 72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.470 Fit side-chains REVERT: B 257 LYS cc_start: 0.9007 (ptmm) cc_final: 0.8693 (ptpt) REVERT: B 260 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: B 275 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 276 GLN cc_start: 0.8766 (tt0) cc_final: 0.8306 (tt0) REVERT: B 310 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: B 318 LYS cc_start: 0.8981 (tttt) cc_final: 0.8694 (tttt) REVERT: L 168 ARG cc_start: 0.8467 (ptm160) cc_final: 0.8104 (tmt90) REVERT: L 169 GLU cc_start: 0.8193 (pp20) cc_final: 0.7819 (pp20) outliers start: 18 outliers final: 10 residues processed: 66 average time/residue: 1.1692 time to fit residues: 80.1022 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 : 0.465 ------------------------------------------------------------------------------- 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 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 143 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071181 restraints weight = 8663.477| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.20 r_work: 0.2955 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4395 Z= 0.178 Angle : 0.514 7.617 5984 Z= 0.272 Chirality : 0.042 0.137 669 Planarity : 0.004 0.041 758 Dihedral : 4.627 43.032 605 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.74 % Allowed : 19.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 552 helix: -0.69 (1.00), residues: 22 sheet: 0.53 (0.33), residues: 260 loop : 0.80 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 142 HIS 0.003 0.001 HIS H 133 PHE 0.010 0.001 PHE B 261 TYR 0.019 0.001 TYR B 286 ARG 0.010 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 163) hydrogen bonds : angle 5.32294 ( 441) SS BOND : bond 0.00143 ( 5) SS BOND : angle 0.52447 ( 10) covalent geometry : bond 0.00416 ( 4390) covalent geometry : angle 0.51393 ( 5974) *********************** 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 70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9002 (ptmm) cc_final: 0.8628 (ptpt) REVERT: B 260 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: B 301 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7951 (mmmm) REVERT: B 310 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8248 (m-10) REVERT: B 317 GLN cc_start: 0.7692 (tt0) cc_final: 0.7110 (mt0) REVERT: B 318 LYS cc_start: 0.8973 (tttt) cc_final: 0.8652 (tttt) REVERT: L 168 ARG cc_start: 0.8458 (ptm160) cc_final: 0.8099 (tmt90) REVERT: L 169 GLU cc_start: 0.8179 (pp20) cc_final: 0.7795 (pp20) outliers start: 18 outliers final: 11 residues processed: 64 average time/residue: 1.1584 time to fit residues: 77.1918 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 143 ILE Chi-restraints excluded: chain L residue 190 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.090718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072557 restraints weight = 8499.445| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.15 r_work: 0.2986 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4395 Z= 0.128 Angle : 0.491 7.212 5984 Z= 0.260 Chirality : 0.042 0.135 669 Planarity : 0.004 0.045 758 Dihedral : 4.447 43.676 605 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.74 % Allowed : 19.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.37), residues: 552 helix: -0.80 (1.01), residues: 23 sheet: 0.58 (0.33), residues: 264 loop : 0.98 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 193 HIS 0.002 0.001 HIS H 133 PHE 0.010 0.001 PHE B 261 TYR 0.019 0.001 TYR B 286 ARG 0.011 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02490 ( 163) hydrogen bonds : angle 5.08164 ( 441) SS BOND : bond 0.00112 ( 5) SS BOND : angle 0.40841 ( 10) covalent geometry : bond 0.00299 ( 4390) covalent geometry : angle 0.49158 ( 5974) *********************** 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 73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9007 (ptmm) cc_final: 0.8627 (ptpt) REVERT: B 260 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: B 275 GLU cc_start: 0.8487 (tp30) cc_final: 0.8009 (tm-30) REVERT: B 310 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8207 (m-10) REVERT: B 317 GLN cc_start: 0.7684 (tt0) cc_final: 0.7128 (mt0) REVERT: B 318 LYS cc_start: 0.8952 (tttt) cc_final: 0.8620 (tttt) REVERT: L 168 ARG cc_start: 0.8455 (ptm160) cc_final: 0.8085 (tmt90) REVERT: L 169 GLU cc_start: 0.8139 (pp20) cc_final: 0.7734 (pp20) outliers start: 18 outliers final: 9 residues processed: 66 average time/residue: 1.1417 time to fit residues: 78.4006 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 : 0.458 ------------------------------------------------------------------------------- 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 L residue 34 SER Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 190 THR 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 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.090980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072897 restraints weight = 8610.021| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.16 r_work: 0.2990 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4395 Z= 0.126 Angle : 0.499 7.045 5984 Z= 0.263 Chirality : 0.042 0.134 669 Planarity : 0.004 0.049 758 Dihedral : 4.062 13.586 604 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.91 % Allowed : 20.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.37), residues: 552 helix: -0.82 (1.01), residues: 23 sheet: 0.62 (0.33), residues: 264 loop : 1.02 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 193 HIS 0.002 0.001 HIS B 285 PHE 0.010 0.001 PHE B 261 TYR 0.019 0.001 TYR B 286 ARG 0.012 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02530 ( 163) hydrogen bonds : angle 5.00524 ( 441) SS BOND : bond 0.00085 ( 5) SS BOND : angle 0.54085 ( 10) covalent geometry : bond 0.00294 ( 4390) covalent geometry : angle 0.49861 ( 5974) *********************** 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 67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.9036 (ptmm) cc_final: 0.8661 (ptpt) REVERT: B 260 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: B 275 GLU cc_start: 0.8474 (tp30) cc_final: 0.8035 (tm-30) REVERT: B 310 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: B 317 GLN cc_start: 0.7701 (tt0) cc_final: 0.7148 (mt0) REVERT: B 318 LYS cc_start: 0.8949 (tttt) cc_final: 0.8619 (tttt) REVERT: L 168 ARG cc_start: 0.8445 (ptm160) cc_final: 0.8075 (tmt90) REVERT: L 169 GLU cc_start: 0.8153 (pp20) cc_final: 0.7750 (pp20) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 1.1916 time to fit residues: 76.8746 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.094442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075061 restraints weight = 8815.256| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.26 r_work: 0.2996 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4395 Z= 0.119 Angle : 0.502 6.895 5984 Z= 0.264 Chirality : 0.042 0.132 669 Planarity : 0.004 0.052 758 Dihedral : 4.043 13.375 604 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.70 % Allowed : 19.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.37), residues: 552 helix: -0.74 (1.02), residues: 23 sheet: 0.68 (0.33), residues: 264 loop : 1.06 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 193 HIS 0.002 0.001 HIS B 285 PHE 0.010 0.001 PHE B 261 TYR 0.010 0.001 TYR H 121 ARG 0.013 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02496 ( 163) hydrogen bonds : angle 4.90659 ( 441) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.48256 ( 10) covalent geometry : bond 0.00280 ( 4390) covalent geometry : angle 0.50192 ( 5974) *********************** 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 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8994 (ptmm) cc_final: 0.8628 (ptpt) REVERT: B 260 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: B 275 GLU cc_start: 0.8485 (tp30) cc_final: 0.8022 (tm-30) REVERT: B 310 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: B 317 GLN cc_start: 0.7686 (tt0) cc_final: 0.7148 (mt0) REVERT: B 318 LYS cc_start: 0.8927 (tttt) cc_final: 0.8414 (tttm) REVERT: L 168 ARG cc_start: 0.8449 (ptm160) cc_final: 0.8074 (tmt90) REVERT: L 169 GLU cc_start: 0.8142 (pp20) cc_final: 0.7730 (pp20) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 1.1870 time to fit residues: 78.9415 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.091487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.073255 restraints weight = 8538.495| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.18 r_work: 0.2997 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4395 Z= 0.133 Angle : 0.510 6.849 5984 Z= 0.268 Chirality : 0.042 0.133 669 Planarity : 0.004 0.054 758 Dihedral : 4.032 12.848 604 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.37), residues: 552 helix: -0.74 (1.00), residues: 23 sheet: 0.68 (0.33), residues: 264 loop : 1.05 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 142 HIS 0.002 0.001 HIS B 285 PHE 0.010 0.001 PHE B 261 TYR 0.011 0.001 TYR H 121 ARG 0.013 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02534 ( 163) hydrogen bonds : angle 4.94674 ( 441) SS BOND : bond 0.00081 ( 5) SS BOND : angle 0.47057 ( 10) covalent geometry : bond 0.00314 ( 4390) covalent geometry : angle 0.50991 ( 5974) ********************** 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 : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8980 (ptmm) cc_final: 0.8599 (ptpt) REVERT: B 260 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 275 GLU cc_start: 0.8483 (tp30) cc_final: 0.8007 (tm-30) REVERT: B 310 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: B 317 GLN cc_start: 0.7678 (tt0) cc_final: 0.7142 (mt0) REVERT: B 318 LYS cc_start: 0.8924 (tttt) cc_final: 0.8399 (tttm) REVERT: L 168 ARG cc_start: 0.8438 (ptm160) cc_final: 0.8063 (tmt90) REVERT: L 169 GLU cc_start: 0.8131 (pp20) cc_final: 0.7848 (pp20) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 1.2018 time to fit residues: 76.1718 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.097219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078104 restraints weight = 8635.569| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.24 r_work: 0.3026 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4395 Z= 0.099 Angle : 0.496 6.743 5984 Z= 0.260 Chirality : 0.042 0.130 669 Planarity : 0.004 0.053 758 Dihedral : 3.894 13.127 604 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.87 % Allowed : 21.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.38), residues: 552 helix: -0.81 (1.00), residues: 23 sheet: 0.78 (0.33), residues: 269 loop : 1.16 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 193 HIS 0.002 0.001 HIS B 285 PHE 0.010 0.001 PHE B 261 TYR 0.008 0.001 TYR H 121 ARG 0.013 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02365 ( 163) hydrogen bonds : angle 4.71093 ( 441) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.35745 ( 10) covalent geometry : bond 0.00233 ( 4390) covalent geometry : angle 0.49633 ( 5974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3171.25 seconds wall clock time: 55 minutes 47.29 seconds (3347.29 seconds total)