Starting phenix.real_space_refine on Sun Apr 27 02:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f9w_31499/04_2025/7f9w_31499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f9w_31499/04_2025/7f9w_31499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f9w_31499/04_2025/7f9w_31499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f9w_31499/04_2025/7f9w_31499.map" model { file = "/net/cci-nas-00/data/ceres_data/7f9w_31499/04_2025/7f9w_31499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f9w_31499/04_2025/7f9w_31499.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 22 5.16 5 C 2654 2.51 5 N 713 2.21 5 O 828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4217 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 bond proxies already assigned to first conformer: 863 Chain: "C" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1669 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 25 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 25 " occ=0.50 Time building chain proxies: 4.05, per 1000 atoms: 0.96 Number of scatterers: 4217 At special positions: 0 Unit cell: (64.26, 64.8, 116.1, 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 22 16.00 O 828 8.00 N 713 7.00 C 2654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 205 " 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: 1.13 Conformation dependent library (CDL) restraints added in 633.8 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.834A pdb=" N VAL C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.700A pdb=" N LEU C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.727A pdb=" N LYS C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.705A pdb=" N GLN A 130 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 145 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.612A pdb=" N TYR A 20 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.878A pdb=" N LEU A 45 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.136A pdb=" N LEU C 11 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 90 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 91 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 41 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.532A pdb=" N THR C 78 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.811A pdb=" N LYS C 36 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.542A pdb=" N VAL C 139 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 138 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 185 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.827A pdb=" N TRP C 154 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 198 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.571A pdb=" N VAL B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 33 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 162 through 163 142 hydrogen bonds defined for protein. 348 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: 1.13 Time building geometry restraints manager: 1.26 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: 1349 1.34 - 1.46: 1038 1.46 - 1.58: 1904 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4322 Sorted by residual: bond pdb=" CB PRO C 147 " pdb=" CG PRO C 147 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.26e+00 bond pdb=" C PHE C 104 " pdb=" N GLY C 105 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.20e-02 6.94e+03 1.23e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 ... (remaining 4317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 5437 1.16 - 2.33: 351 2.33 - 3.49: 68 3.49 - 4.66: 14 4.66 - 5.82: 5 Bond angle restraints: 5875 Sorted by residual: angle pdb=" C GLN C 96 " pdb=" N TYR C 97 " pdb=" CA TYR C 97 " ideal model delta sigma weight residual 122.65 116.83 5.82 1.66e+00 3.63e-01 1.23e+01 angle pdb=" N TYR C 146 " pdb=" CA TYR C 146 " pdb=" C TYR C 146 " ideal model delta sigma weight residual 108.82 103.55 5.27 1.69e+00 3.50e-01 9.74e+00 angle pdb=" C GLU A 111 " pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C HIS B 209 " pdb=" N LYS B 210 " pdb=" CA LYS B 210 " ideal model delta sigma weight residual 120.09 123.62 -3.53 1.25e+00 6.40e-01 7.99e+00 angle pdb=" C LEU B 133 " pdb=" N ALA B 134 " pdb=" CA ALA B 134 " ideal model delta sigma weight residual 120.60 124.34 -3.74 1.53e+00 4.27e-01 5.99e+00 ... (remaining 5870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2385 16.30 - 32.61: 150 32.61 - 48.91: 40 48.91 - 65.21: 3 65.21 - 81.52: 13 Dihedral angle restraints: 2591 sinusoidal: 1004 harmonic: 1587 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual 93.00 159.24 -66.24 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 143.75 -50.75 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA GLU A 113 " pdb=" C GLU A 113 " pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 348 0.027 - 0.054: 182 0.054 - 0.081: 59 0.081 - 0.107: 43 0.107 - 0.134: 14 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA ILE C 54 " pdb=" N ILE C 54 " pdb=" C ILE C 54 " pdb=" CB ILE C 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA TYR C 97 " pdb=" N TYR C 97 " pdb=" C TYR C 97 " pdb=" CB TYR C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 643 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 56 " -0.015 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP C 56 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 56 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 56 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 56 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 56 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 56 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 134 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO B 135 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 155 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 156 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.021 5.00e-02 4.00e+02 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 85 2.67 - 3.23: 3920 3.23 - 3.79: 6053 3.79 - 4.34: 8034 4.34 - 4.90: 13974 Nonbonded interactions: 32066 Sorted by model distance: nonbonded pdb=" OE2 GLU C 111 " pdb=" NE2 GLN C 172 " model vdw 2.114 3.120 nonbonded pdb=" OG SER B 212 " pdb=" OG1 THR B 214 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR A 47 " pdb=" O SER A 54 " model vdw 2.212 3.040 nonbonded pdb=" O SER C 83 " pdb=" NE2 GLN C 85 " model vdw 2.221 3.120 nonbonded pdb=" N GLY A 141 " pdb=" OG SER B 104 " model vdw 2.252 3.120 ... (remaining 32061 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.005 0.049 4328 Z= 0.235 Angle : 0.677 5.819 5887 Z= 0.371 Chirality : 0.043 0.134 646 Planarity : 0.005 0.053 753 Dihedral : 12.990 81.517 1557 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.63 % Allowed : 0.21 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.24 (0.38), residues: 539 helix: 0.20 (1.48), residues: 13 sheet: 0.41 (0.37), residues: 234 loop : 0.05 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 56 HIS 0.002 0.000 HIS B 173 PHE 0.014 0.002 PHE C 145 TYR 0.024 0.002 TYR C 97 ARG 0.004 0.001 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.25634 ( 123) hydrogen bonds : angle 10.10635 ( 348) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.74308 ( 12) covalent geometry : bond 0.00522 ( 4322) covalent geometry : angle 0.67697 ( 5875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.517 Fit side-chains REVERT: A 18 MET cc_start: 0.8747 (mmp) cc_final: 0.8477 (mmt) REVERT: A 26 LEU cc_start: 0.6275 (tt) cc_final: 0.5996 (tt) REVERT: A 45 LEU cc_start: 0.8311 (tp) cc_final: 0.8091 (tt) REVERT: A 106 GLU cc_start: 0.8553 (pp20) cc_final: 0.8322 (pp20) REVERT: A 155 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8381 (tmt170) REVERT: A 160 GLN cc_start: 0.8279 (mm110) cc_final: 0.8026 (mm110) REVERT: C 1 ASP cc_start: 0.8395 (p0) cc_final: 0.8182 (p0) REVERT: C 128 ASP cc_start: 0.8519 (p0) cc_final: 0.8087 (p0) REVERT: C 153 GLN cc_start: 0.7248 (mp10) cc_final: 0.6837 (mp10) REVERT: B 59 ASP cc_start: 0.7667 (t0) cc_final: 0.7417 (t0) REVERT: B 73 ASP cc_start: 0.8333 (t0) cc_final: 0.8130 (t0) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2121 time to fit residues: 24.4070 Evaluate side-chains 83 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN B 6 GLN B 65 GLN B 206 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089011 restraints weight = 26017.115| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 6.74 r_work: 0.3036 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4328 Z= 0.138 Angle : 0.628 6.567 5887 Z= 0.327 Chirality : 0.043 0.151 646 Planarity : 0.005 0.042 753 Dihedral : 4.703 22.127 589 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.63 % Allowed : 5.92 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.52 (0.39), residues: 539 helix: 0.80 (1.56), residues: 13 sheet: 0.53 (0.36), residues: 247 loop : 0.29 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 56 HIS 0.002 0.001 HIS A 103 PHE 0.016 0.001 PHE B 64 TYR 0.017 0.002 TYR C 97 ARG 0.005 0.001 ARG C 217 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 123) hydrogen bonds : angle 6.40805 ( 348) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.60222 ( 12) covalent geometry : bond 0.00308 ( 4322) covalent geometry : angle 0.62830 ( 5875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.501 Fit side-chains REVERT: A 9 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 18 MET cc_start: 0.9012 (mmp) cc_final: 0.8719 (mmt) REVERT: A 126 MET cc_start: 0.8805 (ppp) cc_final: 0.8503 (ppp) REVERT: A 155 ARG cc_start: 0.9024 (ptm-80) cc_final: 0.8708 (tmt170) REVERT: A 160 GLN cc_start: 0.8504 (mm110) cc_final: 0.8105 (mm110) REVERT: C 1 ASP cc_start: 0.8726 (p0) cc_final: 0.8471 (p0) REVERT: C 17 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 176 ASP cc_start: 0.8380 (m-30) cc_final: 0.8000 (t70) REVERT: B 59 ASP cc_start: 0.7751 (t0) cc_final: 0.7502 (t0) REVERT: B 64 PHE cc_start: 0.7800 (m-10) cc_final: 0.7540 (m-10) REVERT: B 73 ASP cc_start: 0.8629 (t0) cc_final: 0.8373 (t0) REVERT: B 100 ARG cc_start: 0.8673 (mtp-110) cc_final: 0.8446 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1771 time to fit residues: 18.9665 Evaluate side-chains 80 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.0060 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089364 restraints weight = 24132.989| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 6.31 r_work: 0.3047 rms_B_bonded: 5.61 restraints_weight: 2.0000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4328 Z= 0.163 Angle : 0.612 6.744 5887 Z= 0.320 Chirality : 0.043 0.164 646 Planarity : 0.004 0.035 753 Dihedral : 4.543 20.667 589 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.69 % Allowed : 9.94 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.54 (0.38), residues: 539 helix: 0.65 (1.56), residues: 13 sheet: 0.61 (0.35), residues: 244 loop : 0.24 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.001 0.000 HIS B 173 PHE 0.008 0.001 PHE B 64 TYR 0.022 0.002 TYR C 97 ARG 0.004 0.001 ARG C 217 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 123) hydrogen bonds : angle 5.70208 ( 348) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.53421 ( 12) covalent geometry : bond 0.00374 ( 4322) covalent geometry : angle 0.61184 ( 5875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.529 Fit side-chains REVERT: A 9 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7448 (tm-30) REVERT: A 18 MET cc_start: 0.8971 (mmp) cc_final: 0.8684 (mmt) REVERT: A 157 THR cc_start: 0.8388 (p) cc_final: 0.8100 (p) REVERT: A 160 GLN cc_start: 0.8485 (mm110) cc_final: 0.8082 (mm110) REVERT: C 1 ASP cc_start: 0.8730 (p0) cc_final: 0.8461 (p0) REVERT: C 17 GLU cc_start: 0.8602 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 176 ASP cc_start: 0.8435 (m-30) cc_final: 0.8071 (t70) REVERT: B 59 ASP cc_start: 0.7778 (t0) cc_final: 0.7505 (t0) REVERT: B 73 ASP cc_start: 0.8619 (t0) cc_final: 0.8340 (t0) REVERT: B 157 GLU cc_start: 0.8555 (pt0) cc_final: 0.8143 (pm20) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.1613 time to fit residues: 17.8434 Evaluate side-chains 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087241 restraints weight = 32938.083| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 7.17 r_work: 0.2989 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4328 Z= 0.185 Angle : 0.623 7.687 5887 Z= 0.323 Chirality : 0.044 0.159 646 Planarity : 0.004 0.034 753 Dihedral : 4.557 22.090 589 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.69 % Allowed : 11.63 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.51 (0.38), residues: 539 helix: 0.56 (1.51), residues: 13 sheet: 0.59 (0.36), residues: 242 loop : 0.22 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 156 HIS 0.001 0.000 HIS B 173 PHE 0.007 0.001 PHE C 215 TYR 0.024 0.002 TYR C 97 ARG 0.005 0.001 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 123) hydrogen bonds : angle 5.49127 ( 348) SS BOND : bond 0.00129 ( 6) SS BOND : angle 0.56240 ( 12) covalent geometry : bond 0.00429 ( 4322) covalent geometry : angle 0.62271 ( 5875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.506 Fit side-chains REVERT: A 9 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 18 MET cc_start: 0.8998 (mmp) cc_final: 0.8674 (mmt) REVERT: A 155 ARG cc_start: 0.8275 (ptm-80) cc_final: 0.7937 (tmt170) REVERT: A 157 THR cc_start: 0.8312 (p) cc_final: 0.8018 (p) REVERT: A 160 GLN cc_start: 0.8501 (mm110) cc_final: 0.8065 (mm110) REVERT: C 1 ASP cc_start: 0.8724 (p0) cc_final: 0.8419 (p0) REVERT: C 17 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 59 ASP cc_start: 0.7804 (t0) cc_final: 0.7519 (t0) REVERT: B 64 PHE cc_start: 0.7165 (m-10) cc_final: 0.6725 (m-10) REVERT: B 73 ASP cc_start: 0.8628 (t0) cc_final: 0.8322 (t0) REVERT: B 157 GLU cc_start: 0.8626 (pt0) cc_final: 0.8157 (pm20) outliers start: 6 outliers final: 5 residues processed: 89 average time/residue: 0.1857 time to fit residues: 20.4874 Evaluate side-chains 87 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.0070 chunk 7 optimal weight: 5.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.129026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.090048 restraints weight = 25032.906| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 6.57 r_work: 0.3068 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4328 Z= 0.106 Angle : 0.578 7.691 5887 Z= 0.297 Chirality : 0.042 0.157 646 Planarity : 0.004 0.031 753 Dihedral : 4.329 22.135 589 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.48 % Allowed : 12.68 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.62 (0.38), residues: 539 helix: 0.73 (1.46), residues: 13 sheet: 0.82 (0.36), residues: 236 loop : 0.15 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 154 HIS 0.002 0.000 HIS C 195 PHE 0.006 0.001 PHE A 121 TYR 0.011 0.001 TYR C 55 ARG 0.004 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 123) hydrogen bonds : angle 5.04419 ( 348) SS BOND : bond 0.00121 ( 6) SS BOND : angle 0.46024 ( 12) covalent geometry : bond 0.00243 ( 4322) covalent geometry : angle 0.57775 ( 5875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7563 (tm-30) REVERT: A 18 MET cc_start: 0.8960 (mmp) cc_final: 0.8632 (mmt) REVERT: A 126 MET cc_start: 0.8797 (ppp) cc_final: 0.8437 (ppp) REVERT: A 144 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 155 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.7930 (tmt170) REVERT: A 157 THR cc_start: 0.8266 (p) cc_final: 0.7923 (p) REVERT: A 160 GLN cc_start: 0.8478 (mm110) cc_final: 0.8053 (mm110) REVERT: C 1 ASP cc_start: 0.8618 (p0) cc_final: 0.8342 (p0) REVERT: C 17 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8026 (tm-30) REVERT: C 176 ASP cc_start: 0.8200 (m-30) cc_final: 0.7780 (t70) REVERT: B 59 ASP cc_start: 0.7749 (t0) cc_final: 0.7479 (t0) REVERT: B 73 ASP cc_start: 0.8584 (t0) cc_final: 0.8291 (t0) REVERT: B 157 GLU cc_start: 0.8577 (pt0) cc_final: 0.8089 (pm20) outliers start: 5 outliers final: 1 residues processed: 91 average time/residue: 0.2023 time to fit residues: 22.9348 Evaluate side-chains 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.124109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086380 restraints weight = 24316.259| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 6.20 r_work: 0.2986 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 4328 Z= 0.274 Angle : 0.658 8.186 5887 Z= 0.346 Chirality : 0.045 0.154 646 Planarity : 0.005 0.041 753 Dihedral : 4.596 20.041 589 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.11 % Allowed : 12.90 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.47 (0.38), residues: 539 helix: 0.39 (1.44), residues: 13 sheet: 0.62 (0.36), residues: 243 loop : 0.14 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 154 HIS 0.002 0.000 HIS B 173 PHE 0.022 0.002 PHE B 64 TYR 0.034 0.002 TYR C 97 ARG 0.005 0.001 ARG C 217 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 123) hydrogen bonds : angle 5.40509 ( 348) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.58466 ( 12) covalent geometry : bond 0.00635 ( 4322) covalent geometry : angle 0.65771 ( 5875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.512 Fit side-chains REVERT: A 9 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 18 MET cc_start: 0.9013 (mmp) cc_final: 0.8632 (mmt) REVERT: A 111 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8907 (mp0) REVERT: A 157 THR cc_start: 0.8336 (p) cc_final: 0.8132 (p) REVERT: A 160 GLN cc_start: 0.8494 (mm110) cc_final: 0.8054 (mm110) REVERT: C 1 ASP cc_start: 0.8709 (p0) cc_final: 0.8376 (p0) REVERT: C 17 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 176 ASP cc_start: 0.8387 (m-30) cc_final: 0.8088 (t70) REVERT: B 59 ASP cc_start: 0.7862 (t0) cc_final: 0.7585 (t0) REVERT: B 73 ASP cc_start: 0.8597 (t0) cc_final: 0.8316 (t0) REVERT: B 157 GLU cc_start: 0.8578 (pt0) cc_final: 0.8158 (pm20) outliers start: 8 outliers final: 5 residues processed: 95 average time/residue: 0.2035 time to fit residues: 23.8051 Evaluate side-chains 91 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.0060 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 34 ASN C 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088304 restraints weight = 27441.614| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 6.61 r_work: 0.3022 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4328 Z= 0.128 Angle : 0.625 8.316 5887 Z= 0.319 Chirality : 0.043 0.151 646 Planarity : 0.004 0.041 753 Dihedral : 4.411 21.072 589 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.69 % Allowed : 14.80 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.47 (0.38), residues: 539 helix: 0.65 (1.42), residues: 13 sheet: 0.69 (0.36), residues: 235 loop : 0.08 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 154 HIS 0.001 0.000 HIS A 139 PHE 0.020 0.001 PHE B 64 TYR 0.016 0.001 TYR C 97 ARG 0.006 0.001 ARG C 217 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 123) hydrogen bonds : angle 5.06181 ( 348) SS BOND : bond 0.00092 ( 6) SS BOND : angle 0.60907 ( 12) covalent geometry : bond 0.00297 ( 4322) covalent geometry : angle 0.62463 ( 5875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.466 Fit side-chains REVERT: A 9 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 18 MET cc_start: 0.9010 (mmp) cc_final: 0.8694 (mmt) REVERT: A 111 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8851 (mp0) REVERT: A 157 THR cc_start: 0.8357 (p) cc_final: 0.8021 (p) REVERT: A 160 GLN cc_start: 0.8486 (mm110) cc_final: 0.8049 (mm110) REVERT: C 1 ASP cc_start: 0.8671 (p0) cc_final: 0.8367 (p0) REVERT: C 17 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 176 ASP cc_start: 0.8262 (m-30) cc_final: 0.7933 (t0) REVERT: C 217 ARG cc_start: 0.7395 (ttp80) cc_final: 0.7062 (mtm110) REVERT: B 59 ASP cc_start: 0.7822 (t0) cc_final: 0.7562 (t0) REVERT: B 73 ASP cc_start: 0.8569 (t0) cc_final: 0.8276 (t0) REVERT: B 157 GLU cc_start: 0.8567 (pt0) cc_final: 0.8077 (pm20) outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 0.1795 time to fit residues: 20.1500 Evaluate side-chains 88 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.0370 chunk 39 optimal weight: 1.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090105 restraints weight = 23490.705| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 6.12 r_work: 0.3064 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4328 Z= 0.123 Angle : 0.616 8.735 5887 Z= 0.313 Chirality : 0.042 0.150 646 Planarity : 0.004 0.034 753 Dihedral : 4.260 20.054 589 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.69 % Allowed : 14.80 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.48 (0.38), residues: 539 helix: 0.58 (1.42), residues: 13 sheet: 0.71 (0.36), residues: 235 loop : 0.07 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 154 HIS 0.001 0.000 HIS C 195 PHE 0.015 0.001 PHE B 64 TYR 0.013 0.001 TYR A 43 ARG 0.005 0.000 ARG C 217 Details of bonding type rmsd hydrogen bonds : bond 0.02734 ( 123) hydrogen bonds : angle 4.90272 ( 348) SS BOND : bond 0.00092 ( 6) SS BOND : angle 0.57160 ( 12) covalent geometry : bond 0.00286 ( 4322) covalent geometry : angle 0.61613 ( 5875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.515 Fit side-chains REVERT: A 9 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 18 MET cc_start: 0.8962 (mmp) cc_final: 0.8655 (mmt) REVERT: A 160 GLN cc_start: 0.8467 (mm110) cc_final: 0.8092 (mm110) REVERT: C 1 ASP cc_start: 0.8650 (p0) cc_final: 0.8361 (p0) REVERT: C 17 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 111 GLU cc_start: 0.8655 (tp30) cc_final: 0.8282 (tt0) REVERT: C 176 ASP cc_start: 0.8276 (m-30) cc_final: 0.7946 (t0) REVERT: C 217 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7170 (mtm110) REVERT: B 59 ASP cc_start: 0.7824 (t0) cc_final: 0.7559 (t0) REVERT: B 73 ASP cc_start: 0.8504 (t0) cc_final: 0.8200 (t0) REVERT: B 157 GLU cc_start: 0.8491 (pt0) cc_final: 0.8023 (pm20) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 0.1673 time to fit residues: 19.3923 Evaluate side-chains 89 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.128653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091663 restraints weight = 20262.215| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 5.77 r_work: 0.3087 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4328 Z= 0.114 Angle : 0.620 9.167 5887 Z= 0.313 Chirality : 0.042 0.145 646 Planarity : 0.004 0.030 753 Dihedral : 4.176 20.075 589 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.06 % Allowed : 15.64 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.50 (0.38), residues: 539 helix: 0.55 (1.39), residues: 13 sheet: 0.70 (0.35), residues: 237 loop : 0.10 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 154 HIS 0.002 0.000 HIS C 195 PHE 0.018 0.001 PHE B 64 TYR 0.011 0.001 TYR C 55 ARG 0.006 0.000 ARG C 217 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 123) hydrogen bonds : angle 4.77508 ( 348) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.52895 ( 12) covalent geometry : bond 0.00265 ( 4322) covalent geometry : angle 0.62015 ( 5875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.475 Fit side-chains REVERT: A 9 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 18 MET cc_start: 0.8936 (mmp) cc_final: 0.8622 (mmt) REVERT: A 160 GLN cc_start: 0.8447 (mm110) cc_final: 0.8082 (mm110) REVERT: C 1 ASP cc_start: 0.8602 (p0) cc_final: 0.8329 (p0) REVERT: C 17 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 111 GLU cc_start: 0.8638 (tp30) cc_final: 0.8330 (tt0) REVERT: C 176 ASP cc_start: 0.8226 (m-30) cc_final: 0.7898 (t0) REVERT: C 217 ARG cc_start: 0.7496 (ttp80) cc_final: 0.7230 (mtm110) REVERT: B 48 MET cc_start: 0.9186 (mmt) cc_final: 0.8706 (mmt) REVERT: B 59 ASP cc_start: 0.7835 (t0) cc_final: 0.7564 (t0) REVERT: B 73 ASP cc_start: 0.8501 (t0) cc_final: 0.8185 (t0) REVERT: B 157 GLU cc_start: 0.8469 (pt0) cc_final: 0.7992 (pm20) outliers start: 3 outliers final: 3 residues processed: 91 average time/residue: 0.1856 time to fit residues: 20.9189 Evaluate side-chains 90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.128168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089840 restraints weight = 21894.492| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 6.07 r_work: 0.3056 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4328 Z= 0.129 Angle : 0.628 9.553 5887 Z= 0.316 Chirality : 0.042 0.146 646 Planarity : 0.004 0.030 753 Dihedral : 4.151 19.204 589 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.69 % Allowed : 16.07 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.48 (0.38), residues: 539 helix: 0.62 (1.41), residues: 13 sheet: 0.71 (0.35), residues: 235 loop : 0.06 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 156 HIS 0.001 0.000 HIS C 195 PHE 0.018 0.001 PHE B 64 TYR 0.015 0.001 TYR A 43 ARG 0.006 0.000 ARG C 217 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 123) hydrogen bonds : angle 4.77408 ( 348) SS BOND : bond 0.00096 ( 6) SS BOND : angle 0.53515 ( 12) covalent geometry : bond 0.00300 ( 4322) covalent geometry : angle 0.62788 ( 5875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 18 MET cc_start: 0.8944 (mmp) cc_final: 0.8621 (mmt) REVERT: A 155 ARG cc_start: 0.8208 (tmt170) cc_final: 0.7902 (ptm-80) REVERT: A 160 GLN cc_start: 0.8457 (mm110) cc_final: 0.8087 (mm110) REVERT: C 1 ASP cc_start: 0.8618 (p0) cc_final: 0.8337 (p0) REVERT: C 17 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 111 GLU cc_start: 0.8656 (tp30) cc_final: 0.8323 (tt0) REVERT: C 176 ASP cc_start: 0.8253 (m-30) cc_final: 0.7929 (t0) REVERT: C 217 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7271 (mtm110) REVERT: B 59 ASP cc_start: 0.7862 (t0) cc_final: 0.7589 (t0) REVERT: B 73 ASP cc_start: 0.8499 (t0) cc_final: 0.8174 (t0) REVERT: B 157 GLU cc_start: 0.8462 (pt0) cc_final: 0.7985 (pm20) outliers start: 6 outliers final: 5 residues processed: 89 average time/residue: 0.1714 time to fit residues: 19.0340 Evaluate side-chains 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.899 > 50: distance: 46 - 104: 15.479 distance: 49 - 101: 18.105 distance: 58 - 88: 18.343 distance: 61 - 85: 21.153 distance: 74 - 79: 25.174 distance: 79 - 80: 9.484 distance: 79 - 224: 23.426 distance: 80 - 81: 12.135 distance: 80 - 83: 27.456 distance: 81 - 82: 32.161 distance: 81 - 85: 25.366 distance: 82 - 221: 29.349 distance: 83 - 84: 16.286 distance: 84 - 231: 20.323 distance: 85 - 86: 8.941 distance: 86 - 87: 9.938 distance: 86 - 89: 16.348 distance: 87 - 88: 11.505 distance: 87 - 93: 18.583 distance: 89 - 90: 13.529 distance: 90 - 91: 16.494 distance: 90 - 92: 28.772 distance: 93 - 94: 4.764 distance: 93 - 211: 13.822 distance: 94 - 95: 13.047 distance: 94 - 97: 12.842 distance: 95 - 96: 20.257 distance: 95 - 101: 23.664 distance: 96 - 208: 24.779 distance: 97 - 98: 10.755 distance: 98 - 99: 23.651 distance: 98 - 100: 33.600 distance: 101 - 102: 11.035 distance: 102 - 103: 22.093 distance: 102 - 105: 22.223 distance: 103 - 104: 8.950 distance: 103 - 109: 7.016 distance: 105 - 106: 16.507 distance: 106 - 107: 24.831 distance: 106 - 108: 22.949 distance: 109 - 110: 18.069 distance: 110 - 111: 9.044 distance: 110 - 113: 23.770 distance: 111 - 112: 31.895 distance: 111 - 117: 18.389 distance: 113 - 114: 13.102 distance: 114 - 115: 29.477 distance: 114 - 116: 16.717 distance: 117 - 118: 16.766 distance: 118 - 119: 10.377 distance: 118 - 121: 13.925 distance: 119 - 120: 10.601 distance: 119 - 128: 3.524 distance: 121 - 122: 9.956 distance: 122 - 123: 7.378 distance: 122 - 124: 7.268 distance: 123 - 125: 24.409 distance: 124 - 126: 8.680 distance: 125 - 127: 11.697 distance: 126 - 127: 13.495 distance: 128 - 129: 15.537 distance: 129 - 130: 11.941 distance: 129 - 132: 24.509 distance: 130 - 131: 32.795 distance: 130 - 140: 25.257 distance: 132 - 133: 14.343 distance: 133 - 134: 13.590 distance: 133 - 135: 7.080 distance: 134 - 136: 11.285 distance: 135 - 137: 16.822 distance: 136 - 138: 9.413 distance: 137 - 138: 9.785 distance: 138 - 139: 10.349 distance: 140 - 141: 11.098 distance: 140 - 146: 7.654 distance: 141 - 142: 17.082 distance: 141 - 144: 45.501 distance: 142 - 143: 20.211 distance: 142 - 147: 6.670 distance: 144 - 145: 21.572 distance: 145 - 146: 37.025 distance: 147 - 148: 10.467 distance: 148 - 149: 11.526 distance: 148 - 151: 14.336 distance: 149 - 150: 14.052 distance: 149 - 158: 22.051 distance: 151 - 152: 23.411 distance: 152 - 153: 11.169 distance: 153 - 154: 6.664 distance: 154 - 155: 10.892 distance: 155 - 156: 14.805 distance: 155 - 157: 12.101 distance: 158 - 159: 8.758 distance: 159 - 160: 5.750 distance: 159 - 162: 7.411 distance: 160 - 161: 17.888 distance: 160 - 167: 11.697 distance: 162 - 163: 8.608 distance: 163 - 164: 6.029 distance: 164 - 165: 8.986