Starting phenix.real_space_refine on Sun Apr 5 04:01:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ly5_63503/04_2026/9ly5_63503_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ly5_63503/04_2026/9ly5_63503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ly5_63503/04_2026/9ly5_63503_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ly5_63503/04_2026/9ly5_63503_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ly5_63503/04_2026/9ly5_63503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ly5_63503/04_2026/9ly5_63503.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 2907 2.51 5 N 786 2.21 5 O 921 1.98 5 H 3200 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7833 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3253 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3224 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "C" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1356 Classifications: {'peptide': 181} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 170} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.14, per 1000 atoms: 0.15 Number of scatterers: 7833 At special positions: 0 Unit cell: (59.44, 89.16, 121.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 921 8.00 N 786 7.00 C 2907 6.00 H 3200 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 193 " distance=2.04 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 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: 0.68 Conformation dependent library (CDL) restraints added in 231.1 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 4.7% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.571A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.675A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 182 through 188 removed outlier: 4.056A pdb=" N HIS B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.999A pdb=" N ILE A 33 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.019A pdb=" N VAL A 107 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.015A pdb=" N TYR A 181 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.015A pdb=" N TYR A 181 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 7.322A pdb=" N ILE B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR B 48 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP B 34 " --> pdb=" O TRP B 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.708A pdb=" N THR B 96 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 117 removed outlier: 6.001A pdb=" N TYR B 172 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.531A pdb=" N VAL B 149 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 77 removed outlier: 6.632A pdb=" N TRP C 67 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 148 removed outlier: 5.778A pdb=" N PHE C 202 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 175 through 179 196 hydrogen bonds defined for protein. 501 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: 1.52 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3199 1.04 - 1.23: 313 1.23 - 1.43: 1700 1.43 - 1.63: 2700 1.63 - 1.83: 24 Bond restraints: 7936 Sorted by residual: bond pdb=" N THR B 68 " pdb=" H THR B 68 " ideal model delta sigma weight residual 0.860 0.942 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CA TYR C 89 " pdb=" C TYR C 89 " ideal model delta sigma weight residual 1.527 1.573 -0.045 1.20e-02 6.94e+03 1.42e+01 bond pdb=" CA SER B 92 " pdb=" CB SER B 92 " ideal model delta sigma weight residual 1.535 1.484 0.051 1.71e-02 3.42e+03 8.97e+00 bond pdb=" N ASP C 154 " pdb=" CA ASP C 154 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.70e+00 bond pdb=" N LEU C 212 " pdb=" CA LEU C 212 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.46e+00 ... (remaining 7931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 13268 1.69 - 3.37: 338 3.37 - 5.06: 70 5.06 - 6.74: 17 6.74 - 8.43: 13 Bond angle restraints: 13706 Sorted by residual: angle pdb=" N ALA C 90 " pdb=" CA ALA C 90 " pdb=" C ALA C 90 " ideal model delta sigma weight residual 112.58 120.65 -8.07 1.22e+00 6.72e-01 4.37e+01 angle pdb=" N VAL C 235 " pdb=" CA VAL C 235 " pdb=" C VAL C 235 " ideal model delta sigma weight residual 108.12 115.96 -7.84 1.44e+00 4.82e-01 2.97e+01 angle pdb=" N ASP C 45 " pdb=" CA ASP C 45 " pdb=" C ASP C 45 " ideal model delta sigma weight residual 110.41 103.96 6.45 1.23e+00 6.61e-01 2.75e+01 angle pdb=" C ALA C 88 " pdb=" CA ALA C 88 " pdb=" CB ALA C 88 " ideal model delta sigma weight residual 111.88 104.66 7.22 1.41e+00 5.03e-01 2.62e+01 angle pdb=" C THR C 93 " pdb=" CA THR C 93 " pdb=" CB THR C 93 " ideal model delta sigma weight residual 110.14 118.17 -8.03 1.60e+00 3.91e-01 2.52e+01 ... (remaining 13701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3487 17.98 - 35.96: 351 35.96 - 53.95: 116 53.95 - 71.93: 22 71.93 - 89.91: 14 Dihedral angle restraints: 3990 sinusoidal: 2006 harmonic: 1984 Sorted by residual: dihedral pdb=" CA TYR B 31 " pdb=" C TYR B 31 " pdb=" N ILE B 32 " pdb=" CA ILE B 32 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 61.63 31.37 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 193 " pdb=" CB CYS B 193 " ideal model delta sinusoidal sigma weight residual 93.00 63.37 29.63 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 3987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 583 0.057 - 0.113: 131 0.113 - 0.170: 22 0.170 - 0.226: 6 0.226 - 0.283: 2 Chirality restraints: 744 Sorted by residual: chirality pdb=" CA SER B 64 " pdb=" N SER B 64 " pdb=" C SER B 64 " pdb=" CB SER B 64 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA LEU A 4 " pdb=" N LEU A 4 " pdb=" C LEU A 4 " pdb=" CB LEU A 4 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA LEU B 135 " pdb=" N LEU B 135 " pdb=" C LEU B 135 " pdb=" CB LEU B 135 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 741 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 1 " 0.137 2.00e-02 2.50e+03 4.30e-01 2.78e+03 pdb=" CD GLN A 1 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN A 1 " -0.130 2.00e-02 2.50e+03 pdb=" NE2 GLN A 1 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 1 " -0.729 2.00e-02 2.50e+03 pdb="HE22 GLN A 1 " 0.738 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 136 " -0.254 2.00e-02 2.50e+03 3.40e-01 1.73e+03 pdb=" CG ASN B 136 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 136 " 0.247 2.00e-02 2.50e+03 pdb=" ND2 ASN B 136 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 136 " 0.526 2.00e-02 2.50e+03 pdb="HD22 ASN B 136 " -0.539 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 137 " 0.236 2.00e-02 2.50e+03 2.82e-01 1.19e+03 pdb=" CG ASN B 137 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 137 " -0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN B 137 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 137 " -0.425 2.00e-02 2.50e+03 pdb="HD22 ASN B 137 " 0.432 2.00e-02 2.50e+03 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 96 2.08 - 2.71: 10706 2.71 - 3.34: 19345 3.34 - 3.97: 27053 3.97 - 4.60: 41232 Nonbonded interactions: 98432 Sorted by model distance: nonbonded pdb=" HE1 TRP B 90 " pdb=" O GLY C 183 " model vdw 1.450 2.450 nonbonded pdb=" HZ3 LYS A 214 " pdb=" OE2 GLU B 122 " model vdw 1.562 2.450 nonbonded pdb="HD21 ASN A 52 " pdb=" OG1 THR A 55 " model vdw 1.566 2.450 nonbonded pdb=" O LYS B 189 " pdb=" H ARG B 210 " model vdw 1.586 2.450 nonbonded pdb=" O ARG B 141 " pdb="HH11 ARG B 141 " model vdw 1.616 2.450 ... (remaining 98427 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: 8.000 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: 0.050 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.700 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:9.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 0.051 4742 Z= 0.304 Angle : 0.882 8.425 6465 Z= 0.551 Chirality : 0.053 0.283 744 Planarity : 0.007 0.118 825 Dihedral : 17.177 89.909 1682 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.62 % Allowed : 25.33 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.34), residues: 598 helix: -0.84 (1.32), residues: 13 sheet: -0.06 (0.30), residues: 299 loop : -1.01 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 156 TYR 0.014 0.002 TYR A 95 PHE 0.020 0.002 PHE B 138 TRP 0.015 0.002 TRP A 103 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 4736) covalent geometry : angle 0.88146 ( 6453) SS BOND : bond 0.00394 ( 6) SS BOND : angle 1.13286 ( 12) hydrogen bonds : bond 0.11659 ( 170) hydrogen bonds : angle 7.13524 ( 501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7507 (mt0) outliers start: 19 outliers final: 12 residues processed: 77 average time/residue: 0.7946 time to fit residues: 64.1654 Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132670 restraints weight = 14051.393| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.41 r_work: 0.3442 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4742 Z= 0.153 Angle : 0.527 5.105 6465 Z= 0.276 Chirality : 0.044 0.138 744 Planarity : 0.005 0.050 825 Dihedral : 5.974 51.511 663 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.67 % Allowed : 26.29 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.34), residues: 598 helix: -0.90 (1.41), residues: 13 sheet: 0.01 (0.30), residues: 295 loop : -0.90 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 141 TYR 0.011 0.001 TYR A 95 PHE 0.010 0.001 PHE B 138 TRP 0.013 0.001 TRP A 103 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4736) covalent geometry : angle 0.52626 ( 6453) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.86212 ( 12) hydrogen bonds : bond 0.03051 ( 170) hydrogen bonds : angle 5.73216 ( 501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7402 (mt0) outliers start: 14 outliers final: 7 residues processed: 66 average time/residue: 0.9004 time to fit residues: 61.9449 Evaluate side-chains 58 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130809 restraints weight = 13918.177| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.47 r_work: 0.3413 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4742 Z= 0.165 Angle : 0.529 5.441 6465 Z= 0.277 Chirality : 0.044 0.134 744 Planarity : 0.005 0.041 825 Dihedral : 5.041 39.715 652 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.86 % Allowed : 25.71 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.34), residues: 598 helix: -1.16 (1.34), residues: 13 sheet: 0.01 (0.30), residues: 295 loop : -0.97 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 141 TYR 0.011 0.001 TYR A 95 PHE 0.011 0.001 PHE C 120 TRP 0.013 0.002 TRP A 103 HIS 0.002 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4736) covalent geometry : angle 0.52799 ( 6453) SS BOND : bond 0.00406 ( 6) SS BOND : angle 0.95780 ( 12) hydrogen bonds : bond 0.02939 ( 170) hydrogen bonds : angle 5.51145 ( 501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7314 (mt0) REVERT: C 44 THR cc_start: 0.8435 (m) cc_final: 0.8090 (p) outliers start: 15 outliers final: 8 residues processed: 68 average time/residue: 0.7895 time to fit residues: 56.3204 Evaluate side-chains 60 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 78 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.0030 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.160894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132604 restraints weight = 14165.422| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.51 r_work: 0.3439 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4742 Z= 0.118 Angle : 0.485 4.830 6465 Z= 0.253 Chirality : 0.043 0.135 744 Planarity : 0.004 0.041 825 Dihedral : 4.495 20.850 650 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.90 % Allowed : 26.67 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.35), residues: 598 helix: -1.14 (1.37), residues: 13 sheet: 0.04 (0.30), residues: 299 loop : -0.82 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 141 TYR 0.010 0.001 TYR A 95 PHE 0.007 0.001 PHE A 171 TRP 0.011 0.001 TRP A 103 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4736) covalent geometry : angle 0.48470 ( 6453) SS BOND : bond 0.00358 ( 6) SS BOND : angle 0.76594 ( 12) hydrogen bonds : bond 0.02564 ( 170) hydrogen bonds : angle 5.18467 ( 501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7270 (mt0) REVERT: C 44 THR cc_start: 0.8463 (m) cc_final: 0.8152 (p) REVERT: C 68 GLN cc_start: 0.6485 (mm110) cc_final: 0.5471 (mt0) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.8199 time to fit residues: 54.9570 Evaluate side-chains 59 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.158993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130856 restraints weight = 14071.148| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.55 r_work: 0.3413 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4742 Z= 0.175 Angle : 0.528 5.466 6465 Z= 0.277 Chirality : 0.044 0.134 744 Planarity : 0.004 0.041 825 Dihedral : 4.652 21.021 650 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.29 % Allowed : 27.43 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.35), residues: 598 helix: -1.21 (1.35), residues: 13 sheet: 0.06 (0.30), residues: 296 loop : -0.89 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.012 0.001 TYR A 95 PHE 0.012 0.002 PHE B 138 TRP 0.014 0.002 TRP A 103 HIS 0.002 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4736) covalent geometry : angle 0.52712 ( 6453) SS BOND : bond 0.00418 ( 6) SS BOND : angle 0.98188 ( 12) hydrogen bonds : bond 0.02876 ( 170) hydrogen bonds : angle 5.36470 ( 501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7358 (tt0) REVERT: C 44 THR cc_start: 0.8449 (m) cc_final: 0.8080 (p) REVERT: C 68 GLN cc_start: 0.6485 (mm110) cc_final: 0.5734 (mm110) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.8111 time to fit residues: 55.2622 Evaluate side-chains 61 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.0060 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.161545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133111 restraints weight = 13934.431| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.50 r_work: 0.3444 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4742 Z= 0.104 Angle : 0.475 4.610 6465 Z= 0.249 Chirality : 0.043 0.136 744 Planarity : 0.004 0.041 825 Dihedral : 4.396 19.028 650 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.52 % Allowed : 28.19 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.35), residues: 598 helix: -1.19 (1.34), residues: 13 sheet: 0.08 (0.29), residues: 299 loop : -0.72 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.009 0.001 TYR A 95 PHE 0.006 0.001 PHE A 171 TRP 0.010 0.001 TRP A 103 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4736) covalent geometry : angle 0.47488 ( 6453) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.72503 ( 12) hydrogen bonds : bond 0.02473 ( 170) hydrogen bonds : angle 5.03542 ( 501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 THR cc_start: 0.8438 (m) cc_final: 0.8156 (p) REVERT: C 68 GLN cc_start: 0.6420 (mm110) cc_final: 0.5530 (mt0) REVERT: C 69 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4345 (tt) REVERT: C 154 ASP cc_start: 0.7185 (m-30) cc_final: 0.6946 (m-30) outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.7990 time to fit residues: 51.9653 Evaluate side-chains 62 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.160193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131901 restraints weight = 14087.996| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.56 r_work: 0.3423 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4742 Z= 0.147 Angle : 0.504 5.094 6465 Z= 0.264 Chirality : 0.043 0.135 744 Planarity : 0.004 0.042 825 Dihedral : 4.481 18.809 650 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.48 % Allowed : 27.62 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.35), residues: 598 helix: -1.20 (1.35), residues: 13 sheet: 0.11 (0.30), residues: 296 loop : -0.82 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.011 0.001 TYR A 95 PHE 0.012 0.001 PHE B 138 TRP 0.012 0.001 TRP A 103 HIS 0.002 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4736) covalent geometry : angle 0.50302 ( 6453) SS BOND : bond 0.00407 ( 6) SS BOND : angle 0.89552 ( 12) hydrogen bonds : bond 0.02690 ( 170) hydrogen bonds : angle 5.13504 ( 501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 THR cc_start: 0.8449 (m) cc_final: 0.8096 (p) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.7438 time to fit residues: 52.4264 Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 95 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130748 restraints weight = 14134.429| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.54 r_work: 0.3410 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4742 Z= 0.183 Angle : 0.537 5.398 6465 Z= 0.282 Chirality : 0.044 0.134 744 Planarity : 0.005 0.042 825 Dihedral : 4.651 19.642 650 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.67 % Allowed : 28.00 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.35), residues: 598 helix: -1.20 (1.36), residues: 13 sheet: 0.09 (0.30), residues: 296 loop : -0.88 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.012 0.002 TYR A 95 PHE 0.013 0.002 PHE B 138 TRP 0.014 0.002 TRP A 103 HIS 0.002 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 4736) covalent geometry : angle 0.53578 ( 6453) SS BOND : bond 0.00422 ( 6) SS BOND : angle 1.01098 ( 12) hydrogen bonds : bond 0.02873 ( 170) hydrogen bonds : angle 5.33164 ( 501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 200 ILE cc_start: 0.8115 (mt) cc_final: 0.7564 (mp) REVERT: C 44 THR cc_start: 0.8456 (m) cc_final: 0.8074 (p) REVERT: C 67 TRP cc_start: 0.7083 (m100) cc_final: 0.6590 (m-90) REVERT: C 68 GLN cc_start: 0.6493 (mm110) cc_final: 0.5630 (mt0) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.7741 time to fit residues: 52.0582 Evaluate side-chains 63 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 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 = 0.3883 r_free = 0.3883 target = 0.160250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131705 restraints weight = 14018.836| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.50 r_work: 0.3424 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4742 Z= 0.134 Angle : 0.505 4.832 6465 Z= 0.265 Chirality : 0.043 0.135 744 Planarity : 0.004 0.041 825 Dihedral : 4.503 18.737 650 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.10 % Allowed : 28.95 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.35), residues: 598 helix: -1.17 (1.36), residues: 13 sheet: 0.13 (0.30), residues: 296 loop : -0.82 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.010 0.001 TYR B 139 PHE 0.010 0.001 PHE B 138 TRP 0.012 0.001 TRP A 103 HIS 0.002 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4736) covalent geometry : angle 0.50368 ( 6453) SS BOND : bond 0.00403 ( 6) SS BOND : angle 0.86433 ( 12) hydrogen bonds : bond 0.02622 ( 170) hydrogen bonds : angle 5.14335 ( 501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6493 (tm-30) REVERT: C 44 THR cc_start: 0.8465 (m) cc_final: 0.8124 (p) REVERT: C 68 GLN cc_start: 0.6468 (mm110) cc_final: 0.5644 (mt0) outliers start: 11 outliers final: 11 residues processed: 61 average time/residue: 0.8423 time to fit residues: 53.9038 Evaluate side-chains 61 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.159978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131402 restraints weight = 13978.941| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.49 r_work: 0.3416 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4742 Z= 0.145 Angle : 0.511 4.951 6465 Z= 0.268 Chirality : 0.043 0.135 744 Planarity : 0.004 0.042 825 Dihedral : 4.506 18.380 650 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.10 % Allowed : 28.95 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.35), residues: 598 helix: -1.19 (1.36), residues: 13 sheet: 0.13 (0.30), residues: 296 loop : -0.84 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.010 0.001 TYR A 95 PHE 0.010 0.001 PHE B 138 TRP 0.013 0.001 TRP A 103 HIS 0.002 0.000 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4736) covalent geometry : angle 0.50957 ( 6453) SS BOND : bond 0.00412 ( 6) SS BOND : angle 0.89595 ( 12) hydrogen bonds : bond 0.02679 ( 170) hydrogen bonds : angle 5.15859 ( 501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ILE cc_start: 0.8101 (mt) cc_final: 0.7554 (mp) REVERT: C 44 THR cc_start: 0.8449 (m) cc_final: 0.8106 (p) REVERT: C 67 TRP cc_start: 0.7053 (m100) cc_final: 0.6578 (m-90) REVERT: C 68 GLN cc_start: 0.6500 (mm110) cc_final: 0.5626 (mt0) outliers start: 11 outliers final: 11 residues processed: 59 average time/residue: 0.8419 time to fit residues: 52.1234 Evaluate side-chains 61 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132690 restraints weight = 14003.232| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.50 r_work: 0.3436 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4742 Z= 0.114 Angle : 0.488 4.544 6465 Z= 0.256 Chirality : 0.043 0.137 744 Planarity : 0.004 0.042 825 Dihedral : 4.358 16.971 650 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.10 % Allowed : 28.76 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.35), residues: 598 helix: -1.14 (1.37), residues: 13 sheet: 0.15 (0.30), residues: 298 loop : -0.74 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.009 0.001 TYR A 95 PHE 0.008 0.001 PHE B 138 TRP 0.010 0.001 TRP A 103 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4736) covalent geometry : angle 0.48767 ( 6453) SS BOND : bond 0.00394 ( 6) SS BOND : angle 0.78295 ( 12) hydrogen bonds : bond 0.02495 ( 170) hydrogen bonds : angle 4.97922 ( 501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.81 seconds wall clock time: 55 minutes 47.52 seconds (3347.52 seconds total)