Starting phenix.real_space_refine on Tue Feb 11 08:21:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qic_13987/02_2025/7qic_13987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qic_13987/02_2025/7qic_13987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qic_13987/02_2025/7qic_13987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qic_13987/02_2025/7qic_13987.map" model { file = "/net/cci-nas-00/data/ceres_data/7qic_13987/02_2025/7qic_13987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qic_13987/02_2025/7qic_13987.cif" } resolution = 4.1 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= 0.001 sd= 0.036 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 Mg 1 5.21 5 S 28 5.16 5 C 3148 2.51 5 N 809 2.21 5 O 855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4841 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2991 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 12, 'TRANS': 388} Chain: "C" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.17, per 1000 atoms: 0.65 Number of scatterers: 4841 At special positions: 0 Unit cell: (88.536, 105.462, 76.818, 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 28 16.00 Mg 1 11.99 O 855 8.00 N 809 7.00 C 3148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 1.18 Conformation dependent library (CDL) restraints added in 588.0 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 55.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.519A pdb=" N THR A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.666A pdb=" N LEU A 74 " --> pdb=" O PHE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.061A pdb=" N ILE A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 144 removed outlier: 3.955A pdb=" N PHE A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 180 through 192 removed outlier: 4.103A pdb=" N THR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.793A pdb=" N PHE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 277 removed outlier: 3.536A pdb=" N GLN A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.851A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 301 through 333 removed outlier: 3.641A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.631A pdb=" N THR A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 removed outlier: 4.261A pdb=" N GLU A 345 " --> pdb=" O LYS A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.570A pdb=" N LYS A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.010A pdb=" N GLN A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.013A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.327A pdb=" N MET A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 437 Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.994A pdb=" N GLU B 111 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 112' Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.998A pdb=" N GLU C 23 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 68 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.816A pdb=" N ALA C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 98 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.859A pdb=" N LEU B 18 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.510A pdb=" N ALA B 50 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 35 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 97 " --> pdb=" O GLY B 35 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 771 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: 1.31 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1530 1.34 - 1.46: 1163 1.46 - 1.58: 2201 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 4942 Sorted by residual: bond pdb=" CA TYR A 168 " pdb=" C TYR A 168 " ideal model delta sigma weight residual 1.523 1.537 -0.013 1.34e-02 5.57e+03 1.00e+00 bond pdb=" CA VAL A 205 " pdb=" CB VAL A 205 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.55e-02 4.16e+03 7.93e-01 bond pdb=" CA TYR A 168 " pdb=" CB TYR A 168 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.05e-01 bond pdb=" CA CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sigma weight residual 1.527 1.548 -0.020 2.48e-02 1.63e+03 6.73e-01 bond pdb=" N TYR A 168 " pdb=" CA TYR A 168 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.67e-01 ... (remaining 4937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6534 1.66 - 3.32: 148 3.32 - 4.98: 28 4.98 - 6.64: 9 6.64 - 8.30: 2 Bond angle restraints: 6721 Sorted by residual: angle pdb=" N GLU B 89 " pdb=" CA GLU B 89 " pdb=" CB GLU B 89 " ideal model delta sigma weight residual 112.78 108.06 4.72 1.53e+00 4.27e-01 9.53e+00 angle pdb=" CA ASN C 83 " pdb=" C ASN C 83 " pdb=" O ASN C 83 " ideal model delta sigma weight residual 121.67 118.16 3.51 1.26e+00 6.30e-01 7.74e+00 angle pdb=" N ASN C 32 " pdb=" CA ASN C 32 " pdb=" C ASN C 32 " ideal model delta sigma weight residual 113.43 110.05 3.38 1.26e+00 6.30e-01 7.21e+00 angle pdb=" C THR A 130 " pdb=" N PHE A 131 " pdb=" CA PHE A 131 " ideal model delta sigma weight residual 120.72 116.25 4.47 1.67e+00 3.59e-01 7.18e+00 angle pdb=" CB MET A 89 " pdb=" CG MET A 89 " pdb=" SD MET A 89 " ideal model delta sigma weight residual 112.70 104.93 7.77 3.00e+00 1.11e-01 6.71e+00 ... (remaining 6716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 2615 15.91 - 31.82: 202 31.82 - 47.73: 61 47.73 - 63.64: 8 63.64 - 79.55: 3 Dihedral angle restraints: 2889 sinusoidal: 1068 harmonic: 1821 Sorted by residual: dihedral pdb=" CA GLN B 117 " pdb=" C GLN B 117 " pdb=" N GLY B 118 " pdb=" CA GLY B 118 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+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 93.00 124.62 -31.62 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA VAL C 28 " pdb=" C VAL C 28 " pdb=" N PHE C 29 " pdb=" CA PHE C 29 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 476 0.036 - 0.071: 238 0.071 - 0.106: 66 0.106 - 0.142: 13 0.142 - 0.177: 2 Chirality restraints: 795 Sorted by residual: chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR C 90 " pdb=" CA THR C 90 " pdb=" OG1 THR C 90 " pdb=" CG2 THR C 90 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA PRO A 228 " pdb=" N PRO A 228 " pdb=" C PRO A 228 " pdb=" CB PRO A 228 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 792 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 13 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO C 14 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 309 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLY A 309 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 309 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " 0.014 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE A 131 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.001 2.00e-02 2.50e+03 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 694 2.76 - 3.29: 4843 3.29 - 3.83: 7905 3.83 - 4.36: 8604 4.36 - 4.90: 15115 Nonbonded interactions: 37161 Sorted by model distance: nonbonded pdb=" O TYR B 94 " pdb=" OG1 THR B 119 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 103 " model vdw 2.269 3.040 nonbonded pdb=" O ASN A 126 " pdb=" OG1 THR A 130 " model vdw 2.296 3.040 nonbonded pdb=" O ARG B 52 " pdb=" NH1 ARG B 72 " model vdw 2.306 3.120 nonbonded pdb=" OG1 THR A 129 " pdb=" ND2 ASN A 382 " model vdw 2.341 3.120 ... (remaining 37156 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.370 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4942 Z= 0.193 Angle : 0.650 8.303 6721 Z= 0.350 Chirality : 0.043 0.177 795 Planarity : 0.005 0.067 837 Dihedral : 12.831 79.553 1717 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.34), residues: 633 helix: 0.77 (0.30), residues: 305 sheet: -1.57 (0.63), residues: 73 loop : -1.78 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 160 HIS 0.001 0.000 HIS A 207 PHE 0.030 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.009 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.513 Fit side-chains REVERT: A 120 LEU cc_start: 0.7446 (tt) cc_final: 0.7147 (mm) REVERT: A 182 PHE cc_start: 0.6387 (m-10) cc_final: 0.6106 (m-10) REVERT: A 246 LYS cc_start: 0.8682 (tttm) cc_final: 0.8177 (tptt) REVERT: C 14 PRO cc_start: 0.8515 (Cg_endo) cc_final: 0.8214 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1613 time to fit residues: 30.0593 Evaluate side-chains 119 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.159102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130409 restraints weight = 7155.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130811 restraints weight = 6615.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130863 restraints weight = 7014.763| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4942 Z= 0.225 Angle : 0.601 5.989 6721 Z= 0.318 Chirality : 0.044 0.184 795 Planarity : 0.005 0.052 837 Dihedral : 4.305 21.560 686 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.69 % Favored : 91.15 % Rotamer: Outliers : 0.40 % Allowed : 5.98 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.34), residues: 633 helix: 1.17 (0.29), residues: 316 sheet: -1.39 (0.65), residues: 73 loop : -1.89 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.001 0.001 HIS A 300 PHE 0.033 0.002 PHE A 131 TYR 0.014 0.001 TYR A 185 ARG 0.006 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.473 Fit side-chains REVERT: A 80 MET cc_start: 0.8652 (mmp) cc_final: 0.8301 (mmt) REVERT: A 142 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 143 MET cc_start: 0.8633 (tpp) cc_final: 0.8231 (tpp) REVERT: A 191 MET cc_start: 0.6934 (ttp) cc_final: 0.6702 (ttp) REVERT: A 246 LYS cc_start: 0.8801 (tttm) cc_final: 0.8271 (tptt) REVERT: A 319 CYS cc_start: 0.8122 (m) cc_final: 0.7840 (t) REVERT: C 47 LEU cc_start: 0.8408 (tp) cc_final: 0.8108 (tp) REVERT: B 37 PHE cc_start: 0.8483 (m-80) cc_final: 0.8255 (m-80) REVERT: B 47 PHE cc_start: 0.8665 (t80) cc_final: 0.8395 (t80) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1634 time to fit residues: 29.3885 Evaluate side-chains 117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 382 ASN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.156115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.136718 restraints weight = 6526.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137606 restraints weight = 5456.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.138174 restraints weight = 4863.443| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4942 Z= 0.197 Angle : 0.585 5.969 6721 Z= 0.311 Chirality : 0.043 0.183 795 Planarity : 0.004 0.054 837 Dihedral : 4.308 21.814 686 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.06 % Favored : 91.79 % Rotamer: Outliers : 0.20 % Allowed : 2.79 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.34), residues: 633 helix: 1.24 (0.29), residues: 316 sheet: -1.41 (0.64), residues: 73 loop : -1.91 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.016 0.002 PHE C 50 TYR 0.010 0.001 TYR A 185 ARG 0.003 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.8800 (mmp) cc_final: 0.8322 (mmt) REVERT: A 246 LYS cc_start: 0.8559 (tttm) cc_final: 0.8208 (tptt) REVERT: A 252 LYS cc_start: 0.7898 (tptm) cc_final: 0.7374 (ttpt) REVERT: A 319 CYS cc_start: 0.8310 (m) cc_final: 0.8107 (t) REVERT: C 47 LEU cc_start: 0.8411 (tp) cc_final: 0.8121 (tp) REVERT: B 47 PHE cc_start: 0.8549 (t80) cc_final: 0.8335 (t80) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1477 time to fit residues: 26.6816 Evaluate side-chains 122 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 0.0170 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.155145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.135741 restraints weight = 6591.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.136619 restraints weight = 5491.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136936 restraints weight = 4859.812| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4942 Z= 0.202 Angle : 0.579 5.812 6721 Z= 0.304 Chirality : 0.043 0.180 795 Planarity : 0.004 0.055 837 Dihedral : 4.270 22.192 686 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.37 % Favored : 91.47 % Rotamer: Outliers : 0.20 % Allowed : 3.39 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.34), residues: 633 helix: 1.39 (0.29), residues: 310 sheet: -1.72 (0.58), residues: 84 loop : -1.78 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.001 HIS A 300 PHE 0.018 0.001 PHE A 131 TYR 0.013 0.001 TYR A 185 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8556 (tttm) cc_final: 0.8140 (tptt) REVERT: A 319 CYS cc_start: 0.8351 (m) cc_final: 0.8147 (t) REVERT: C 14 PRO cc_start: 0.8803 (Cg_exo) cc_final: 0.8162 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6701 (tp-100) cc_final: 0.6492 (tp-100) REVERT: C 47 LEU cc_start: 0.8402 (tp) cc_final: 0.8163 (tp) REVERT: B 47 PHE cc_start: 0.8581 (t80) cc_final: 0.8316 (t80) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1417 time to fit residues: 25.5481 Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 58 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.154950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.136866 restraints weight = 6629.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136034 restraints weight = 6724.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136539 restraints weight = 6461.837| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4942 Z= 0.209 Angle : 0.588 5.663 6721 Z= 0.308 Chirality : 0.043 0.175 795 Planarity : 0.004 0.056 837 Dihedral : 4.299 21.942 686 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.20 % Allowed : 2.39 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.34), residues: 633 helix: 1.40 (0.29), residues: 312 sheet: -1.62 (0.59), residues: 84 loop : -1.87 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.001 0.001 HIS A 300 PHE 0.022 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8556 (tttm) cc_final: 0.8163 (tptt) REVERT: A 252 LYS cc_start: 0.7985 (tptm) cc_final: 0.7498 (ttpt) REVERT: A 319 CYS cc_start: 0.8385 (m) cc_final: 0.8110 (t) REVERT: C 14 PRO cc_start: 0.8840 (Cg_exo) cc_final: 0.8241 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6479 (tp-100) cc_final: 0.6261 (tp-100) REVERT: B 47 PHE cc_start: 0.8574 (t80) cc_final: 0.8236 (t80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1310 time to fit residues: 23.2094 Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 0.0170 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 0.0970 chunk 6 optimal weight: 0.2980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.161791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135214 restraints weight = 7232.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.134867 restraints weight = 6916.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135418 restraints weight = 8042.711| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4942 Z= 0.178 Angle : 0.571 5.529 6721 Z= 0.298 Chirality : 0.042 0.172 795 Planarity : 0.005 0.073 837 Dihedral : 4.225 21.807 686 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.20 % Allowed : 2.59 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.34), residues: 633 helix: 1.49 (0.29), residues: 312 sheet: -1.56 (0.59), residues: 84 loop : -1.85 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.023 0.001 PHE A 131 TYR 0.008 0.001 TYR A 185 ARG 0.007 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.531 Fit side-chains REVERT: A 51 MET cc_start: 0.7435 (tmm) cc_final: 0.7075 (tmm) REVERT: A 89 MET cc_start: 0.7757 (tpt) cc_final: 0.7424 (ttp) REVERT: A 246 LYS cc_start: 0.8719 (tttm) cc_final: 0.8260 (tptt) REVERT: A 252 LYS cc_start: 0.7900 (tptm) cc_final: 0.7647 (ttpt) REVERT: A 319 CYS cc_start: 0.8459 (m) cc_final: 0.8119 (t) REVERT: C 14 PRO cc_start: 0.8864 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6529 (tp-100) cc_final: 0.6306 (tp-100) REVERT: C 58 ASN cc_start: 0.8711 (p0) cc_final: 0.8338 (p0) REVERT: B 47 PHE cc_start: 0.8549 (t80) cc_final: 0.8218 (t80) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1362 time to fit residues: 25.3086 Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.161434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134210 restraints weight = 7163.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133422 restraints weight = 6067.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.134147 restraints weight = 6330.438| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4942 Z= 0.199 Angle : 0.612 6.569 6721 Z= 0.314 Chirality : 0.043 0.195 795 Planarity : 0.005 0.058 837 Dihedral : 4.237 21.541 686 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.20 % Allowed : 1.79 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.34), residues: 633 helix: 1.55 (0.29), residues: 312 sheet: -1.50 (0.60), residues: 84 loop : -1.85 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.023 0.001 PHE A 327 TYR 0.008 0.001 TYR A 185 ARG 0.007 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.474 Fit side-chains REVERT: A 89 MET cc_start: 0.7758 (tpt) cc_final: 0.7476 (ttp) REVERT: A 246 LYS cc_start: 0.8771 (tttm) cc_final: 0.8252 (tptt) REVERT: A 319 CYS cc_start: 0.8378 (m) cc_final: 0.8001 (t) REVERT: C 14 PRO cc_start: 0.8780 (Cg_exo) cc_final: 0.8294 (Cg_endo) REVERT: C 30 MET cc_start: 0.7150 (ptm) cc_final: 0.6885 (ptm) REVERT: C 58 ASN cc_start: 0.8722 (p0) cc_final: 0.8357 (p0) REVERT: B 47 PHE cc_start: 0.8682 (t80) cc_final: 0.8379 (t80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1257 time to fit residues: 22.4110 Evaluate side-chains 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 53 optimal weight: 0.0570 chunk 11 optimal weight: 0.0000 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.165402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.138534 restraints weight = 7124.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138106 restraints weight = 6194.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138826 restraints weight = 5874.207| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4942 Z= 0.172 Angle : 0.588 7.307 6721 Z= 0.304 Chirality : 0.042 0.175 795 Planarity : 0.005 0.063 837 Dihedral : 4.204 21.244 686 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.20 % Allowed : 1.39 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.35), residues: 633 helix: 1.70 (0.29), residues: 314 sheet: -1.52 (0.60), residues: 84 loop : -1.85 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.015 0.001 PHE B 29 TYR 0.021 0.001 TYR A 185 ARG 0.007 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.536 Fit side-chains REVERT: A 89 MET cc_start: 0.7776 (tpt) cc_final: 0.7508 (ttp) REVERT: A 319 CYS cc_start: 0.8385 (m) cc_final: 0.8160 (t) REVERT: A 385 ILE cc_start: 0.7892 (tp) cc_final: 0.7618 (tp) REVERT: C 14 PRO cc_start: 0.8799 (Cg_exo) cc_final: 0.8331 (Cg_endo) REVERT: C 30 MET cc_start: 0.6814 (ptm) cc_final: 0.6429 (ptm) REVERT: C 58 ASN cc_start: 0.8524 (p0) cc_final: 0.8129 (p0) REVERT: B 47 PHE cc_start: 0.8581 (t80) cc_final: 0.8341 (t80) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.1269 time to fit residues: 24.3491 Evaluate side-chains 122 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.162683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135430 restraints weight = 6967.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134855 restraints weight = 5939.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135931 restraints weight = 5676.395| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4942 Z= 0.196 Angle : 0.592 8.052 6721 Z= 0.311 Chirality : 0.043 0.182 795 Planarity : 0.005 0.061 837 Dihedral : 4.233 21.255 686 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.35), residues: 633 helix: 1.69 (0.29), residues: 311 sheet: -1.50 (0.58), residues: 90 loop : -1.65 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.001 0.001 HIS B 31 PHE 0.013 0.001 PHE A 131 TYR 0.008 0.001 TYR A 185 ARG 0.008 0.001 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.535 Fit side-chains REVERT: A 89 MET cc_start: 0.7799 (tpt) cc_final: 0.7539 (ttp) REVERT: A 319 CYS cc_start: 0.8345 (m) cc_final: 0.8084 (t) REVERT: A 385 ILE cc_start: 0.7921 (tp) cc_final: 0.7628 (tp) REVERT: C 14 PRO cc_start: 0.8780 (Cg_exo) cc_final: 0.8333 (Cg_endo) REVERT: C 30 MET cc_start: 0.6952 (ptm) cc_final: 0.6639 (ptm) REVERT: C 58 ASN cc_start: 0.8700 (p0) cc_final: 0.8354 (p0) REVERT: B 47 PHE cc_start: 0.8641 (t80) cc_final: 0.8333 (t80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1299 time to fit residues: 24.3510 Evaluate side-chains 118 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.160106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130183 restraints weight = 7184.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132178 restraints weight = 5606.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.133556 restraints weight = 4760.308| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4942 Z= 0.231 Angle : 0.641 7.580 6721 Z= 0.329 Chirality : 0.044 0.182 795 Planarity : 0.005 0.061 837 Dihedral : 4.236 21.341 686 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.35), residues: 633 helix: 1.64 (0.29), residues: 311 sheet: -1.56 (0.61), residues: 84 loop : -1.77 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.002 0.001 HIS B 31 PHE 0.016 0.002 PHE A 131 TYR 0.021 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.481 Fit side-chains REVERT: A 89 MET cc_start: 0.7814 (tpt) cc_final: 0.7538 (ttp) REVERT: A 246 LYS cc_start: 0.8638 (tttp) cc_final: 0.8194 (tptt) REVERT: A 319 CYS cc_start: 0.8344 (m) cc_final: 0.8062 (t) REVERT: A 385 ILE cc_start: 0.7928 (tp) cc_final: 0.7651 (tp) REVERT: C 14 PRO cc_start: 0.8770 (Cg_exo) cc_final: 0.8438 (Cg_endo) REVERT: C 58 ASN cc_start: 0.8788 (p0) cc_final: 0.8162 (p0) REVERT: B 47 PHE cc_start: 0.8648 (t80) cc_final: 0.8387 (t80) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1278 time to fit residues: 23.5233 Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.0010 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.163910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.135645 restraints weight = 7119.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.136055 restraints weight = 6232.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.136242 restraints weight = 6153.681| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4942 Z= 0.182 Angle : 0.616 8.100 6721 Z= 0.316 Chirality : 0.043 0.176 795 Planarity : 0.005 0.061 837 Dihedral : 4.195 20.755 686 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.35), residues: 633 helix: 1.74 (0.29), residues: 313 sheet: -1.50 (0.61), residues: 84 loop : -1.65 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.001 0.001 HIS B 31 PHE 0.013 0.001 PHE A 131 TYR 0.012 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.77 seconds wall clock time: 30 minutes 57.06 seconds (1857.06 seconds total)