Starting phenix.real_space_refine on Thu Jun 5 01:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qic_13987/06_2025/7qic_13987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qic_13987/06_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_13987/06_2025/7qic_13987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qic_13987/06_2025/7qic_13987.map" model { file = "/net/cci-nas-00/data/ceres_data/7qic_13987/06_2025/7qic_13987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qic_13987/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 3.62, per 1000 atoms: 0.75 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: 1.35 Conformation dependent library (CDL) restraints added in 640.4 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: 0.54 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: 1.32 Time building geometry restraints manager: 1.60 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.580 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- 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 4944 Z= 0.135 Angle : 0.650 8.303 6725 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 Details of bonding type rmsd hydrogen bonds : bond 0.17168 ( 267) hydrogen bonds : angle 6.88654 ( 771) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.58431 ( 4) covalent geometry : bond 0.00288 ( 4942) covalent geometry : angle 0.65041 ( 6721) *********************** 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 : 0.518 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: 0.1560 time to fit residues: 29.0821 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 : 0.534 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.6780 ------------------------------------------------------------------------------- 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 C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.159563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.132773 restraints weight = 7158.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131763 restraints weight = 6364.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132081 restraints weight = 7030.422| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4944 Z= 0.148 Angle : 0.598 5.958 6725 Z= 0.318 Chirality : 0.043 0.183 795 Planarity : 0.005 0.053 837 Dihedral : 4.281 21.409 686 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.21 % Favored : 91.63 % Rotamer: Outliers : 0.40 % Allowed : 5.78 % Favored : 93.82 % 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: -0.35 (0.34), residues: 633 helix: 1.24 (0.29), residues: 314 sheet: -1.37 (0.65), residues: 73 loop : -1.83 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.001 0.001 HIS A 300 PHE 0.033 0.001 PHE A 131 TYR 0.014 0.001 TYR A 185 ARG 0.007 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 267) hydrogen bonds : angle 5.15237 ( 771) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.52400 ( 4) covalent geometry : bond 0.00335 ( 4942) covalent geometry : angle 0.59822 ( 6721) *********************** 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 : 0.494 Fit side-chains REVERT: A 80 MET cc_start: 0.8614 (mmp) cc_final: 0.8351 (mmt) REVERT: A 191 MET cc_start: 0.7049 (ttp) cc_final: 0.6840 (ttp) REVERT: A 246 LYS cc_start: 0.8789 (tttm) cc_final: 0.8267 (tptt) REVERT: A 319 CYS cc_start: 0.8140 (m) cc_final: 0.7854 (t) REVERT: C 47 LEU cc_start: 0.8411 (tp) cc_final: 0.8115 (tp) REVERT: B 47 PHE cc_start: 0.8653 (t80) cc_final: 0.8335 (t80) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1656 time to fit residues: 29.8957 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 : 0.481 ------------------------------------------------------------------------------- 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: 0.0040 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN 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 = 0.3679 r_free = 0.3679 target = 0.157266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.137443 restraints weight = 6506.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.138366 restraints weight = 5463.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139187 restraints weight = 4858.350| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4944 Z= 0.128 Angle : 0.580 5.927 6725 Z= 0.309 Chirality : 0.043 0.188 795 Planarity : 0.004 0.054 837 Dihedral : 4.317 21.624 686 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.81 % 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: 1.25 (0.29), residues: 316 sheet: -1.71 (0.57), residues: 84 loop : -1.86 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.016 0.002 PHE C 50 TYR 0.009 0.001 TYR C 93 ARG 0.005 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 267) hydrogen bonds : angle 4.80937 ( 771) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.58318 ( 4) covalent geometry : bond 0.00283 ( 4942) covalent geometry : angle 0.58036 ( 6721) *********************** 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 135 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8793 (mmp) cc_final: 0.8314 (mmt) REVERT: A 246 LYS cc_start: 0.8545 (tttm) cc_final: 0.8173 (tptt) REVERT: C 47 LEU cc_start: 0.8388 (tp) cc_final: 0.8102 (tp) REVERT: B 47 PHE cc_start: 0.8522 (t80) cc_final: 0.8176 (t80) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1465 time to fit residues: 25.8475 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 : 0.461 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 55 optimal weight: 0.0010 chunk 54 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.3744 ------------------------------------------------------------------------------- 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 13 GLN C 32 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 = 0.3689 r_free = 0.3689 target = 0.157991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.138753 restraints weight = 6572.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.139658 restraints weight = 5452.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140335 restraints weight = 4822.400| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4944 Z= 0.121 Angle : 0.566 5.704 6725 Z= 0.298 Chirality : 0.043 0.178 795 Planarity : 0.004 0.055 837 Dihedral : 4.228 22.101 686 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % 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: -0.30 (0.34), residues: 633 helix: 1.41 (0.29), residues: 310 sheet: -1.69 (0.58), residues: 84 loop : -1.79 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.001 0.000 HIS A 300 PHE 0.018 0.001 PHE A 131 TYR 0.012 0.001 TYR A 185 ARG 0.006 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 267) hydrogen bonds : angle 4.58687 ( 771) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.31593 ( 4) covalent geometry : bond 0.00267 ( 4942) covalent geometry : angle 0.56582 ( 6721) *********************** 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 135 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.580 Fit side-chains REVERT: A 80 MET cc_start: 0.8813 (mmp) cc_final: 0.8300 (mmt) REVERT: C 14 PRO cc_start: 0.8807 (Cg_exo) cc_final: 0.8150 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6670 (tp-100) cc_final: 0.6457 (tp-100) REVERT: C 47 LEU cc_start: 0.8338 (tp) cc_final: 0.8116 (tp) REVERT: B 47 PHE cc_start: 0.8499 (t80) cc_final: 0.8230 (t80) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1657 time to fit residues: 29.8576 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 : 0.497 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 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 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 = 0.3656 r_free = 0.3656 target = 0.154700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136283 restraints weight = 6661.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135395 restraints weight = 6621.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135783 restraints weight = 6943.159| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4944 Z= 0.143 Angle : 0.582 5.697 6725 Z= 0.307 Chirality : 0.043 0.176 795 Planarity : 0.004 0.056 837 Dihedral : 4.272 22.036 686 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.20 % Allowed : 1.99 % Favored : 97.81 % 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: -0.32 (0.34), residues: 633 helix: 1.38 (0.29), residues: 312 sheet: -1.52 (0.60), residues: 84 loop : -1.90 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.001 0.001 HIS A 300 PHE 0.023 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.005 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 267) hydrogen bonds : angle 4.50285 ( 771) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.48791 ( 4) covalent geometry : bond 0.00330 ( 4942) covalent geometry : angle 0.58161 ( 6721) *********************** 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 133 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8443 (tttp) cc_final: 0.8146 (tptt) REVERT: C 14 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8173 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6459 (tp-100) cc_final: 0.6230 (tp-100) REVERT: B 47 PHE cc_start: 0.8540 (t80) cc_final: 0.8239 (t80) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1503 time to fit residues: 26.6621 Evaluate side-chains 113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 0.0000 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 0.0030 chunk 6 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.158320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138864 restraints weight = 6652.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.139897 restraints weight = 5561.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140496 restraints weight = 4874.739| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4944 Z= 0.120 Angle : 0.586 6.647 6725 Z= 0.301 Chirality : 0.042 0.170 795 Planarity : 0.005 0.072 837 Dihedral : 4.196 21.869 686 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.20 % Allowed : 3.19 % Favored : 96.61 % 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: -0.23 (0.34), residues: 633 helix: 1.48 (0.29), residues: 312 sheet: -1.53 (0.59), residues: 84 loop : -1.88 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 267) hydrogen bonds : angle 4.43431 ( 771) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.30507 ( 4) covalent geometry : bond 0.00265 ( 4942) covalent geometry : angle 0.58622 ( 6721) *********************** 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 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.7381 (tmm) cc_final: 0.7010 (tmm) REVERT: C 14 PRO cc_start: 0.8855 (Cg_exo) cc_final: 0.8245 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6496 (tp-100) cc_final: 0.6278 (tp-100) REVERT: C 58 ASN cc_start: 0.8616 (p0) cc_final: 0.8239 (p0) REVERT: B 47 PHE cc_start: 0.8462 (t80) cc_final: 0.8258 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1351 time to fit residues: 24.7908 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 : 0.527 ------------------------------------------------------------------------------- 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: 0.1980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 11 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 0.0010 overall best weight: 0.2022 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.166342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139962 restraints weight = 7071.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139208 restraints weight = 6375.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.139720 restraints weight = 6438.468| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4944 Z= 0.114 Angle : 0.599 7.582 6725 Z= 0.305 Chirality : 0.042 0.184 795 Planarity : 0.005 0.058 837 Dihedral : 4.138 21.360 686 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.20 % Allowed : 1.00 % Favored : 98.80 % 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: -0.07 (0.34), residues: 633 helix: 1.61 (0.29), residues: 315 sheet: -1.41 (0.61), residues: 79 loop : -1.86 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.020 0.001 PHE A 327 TYR 0.008 0.001 TYR A 185 ARG 0.007 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 267) hydrogen bonds : angle 4.37801 ( 771) SS BOND : bond 0.00184 ( 2) SS BOND : angle 0.25026 ( 4) covalent geometry : bond 0.00240 ( 4942) covalent geometry : angle 0.59914 ( 6721) *********************** 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 142 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8010 (tptm) cc_final: 0.7765 (tptt) REVERT: A 385 ILE cc_start: 0.8154 (tp) cc_final: 0.7813 (tp) REVERT: C 14 PRO cc_start: 0.8838 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6540 (tp-100) cc_final: 0.6333 (tp-100) REVERT: C 58 ASN cc_start: 0.8488 (p0) cc_final: 0.8108 (p0) REVERT: C 79 TYR cc_start: 0.8639 (m-80) cc_final: 0.8408 (m-10) REVERT: B 47 PHE cc_start: 0.8486 (t80) cc_final: 0.8249 (t80) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1377 time to fit residues: 26.7064 Evaluate side-chains 120 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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: 0.0470 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 11 optimal weight: 0.0670 chunk 3 optimal weight: 0.4980 chunk 30 optimal weight: 0.0370 chunk 58 optimal weight: 0.0040 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.0344 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.169254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140102 restraints weight = 7025.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.141493 restraints weight = 6164.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.142503 restraints weight = 5036.695| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4944 Z= 0.113 Angle : 0.592 6.749 6725 Z= 0.301 Chirality : 0.042 0.171 795 Planarity : 0.005 0.059 837 Dihedral : 4.093 21.473 686 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: -0.05 (0.34), residues: 633 helix: 1.67 (0.29), residues: 316 sheet: -1.41 (0.61), residues: 79 loop : -1.95 (0.39), residues: 238 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 0.016 0.001 PHE B 29 TYR 0.019 0.001 TYR A 185 ARG 0.007 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 267) hydrogen bonds : angle 4.30774 ( 771) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.20492 ( 4) covalent geometry : bond 0.00232 ( 4942) covalent geometry : angle 0.59189 ( 6721) *********************** 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 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.908 Fit side-chains REVERT: A 252 LYS cc_start: 0.8001 (tptm) cc_final: 0.7663 (ttpt) REVERT: A 372 MET cc_start: 0.8906 (mmm) cc_final: 0.8494 (tpt) REVERT: A 385 ILE cc_start: 0.8008 (tp) cc_final: 0.7641 (tp) REVERT: C 14 PRO cc_start: 0.8787 (Cg_exo) cc_final: 0.8320 (Cg_endo) REVERT: C 53 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7813 (ttm110) REVERT: C 58 ASN cc_start: 0.8041 (p0) cc_final: 0.7630 (p0) REVERT: C 79 TYR cc_start: 0.8557 (m-80) cc_final: 0.8318 (m-10) REVERT: B 47 PHE cc_start: 0.8597 (t80) cc_final: 0.8332 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1453 time to fit residues: 27.1216 Evaluate side-chains 121 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.157871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.136135 restraints weight = 6442.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.137144 restraints weight = 5315.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138106 restraints weight = 4685.589| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4944 Z= 0.153 Angle : 0.632 8.258 6725 Z= 0.327 Chirality : 0.043 0.187 795 Planarity : 0.005 0.060 837 Dihedral : 4.192 21.408 686 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % 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: -0.12 (0.34), residues: 633 helix: 1.61 (0.29), residues: 316 sheet: -1.58 (0.60), residues: 84 loop : -1.91 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 53 HIS 0.002 0.001 HIS B 31 PHE 0.018 0.002 PHE C 50 TYR 0.011 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 267) hydrogen bonds : angle 4.36676 ( 771) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.41597 ( 4) covalent geometry : bond 0.00357 ( 4942) covalent geometry : angle 0.63237 ( 6721) *********************** 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 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.552 Fit side-chains REVERT: A 385 ILE cc_start: 0.7866 (tp) cc_final: 0.7638 (tp) REVERT: C 14 PRO cc_start: 0.8795 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: C 30 MET cc_start: 0.8463 (pmm) cc_final: 0.6859 (ptm) REVERT: C 58 ASN cc_start: 0.8783 (p0) cc_final: 0.8409 (p0) REVERT: B 47 PHE cc_start: 0.8629 (t80) cc_final: 0.8385 (t80) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1610 time to fit residues: 29.6959 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 : 0.828 ------------------------------------------------------------------------------- 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: 0.8980 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3731 r_free = 0.3731 target = 0.161957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.131863 restraints weight = 7126.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.134171 restraints weight = 5395.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.135546 restraints weight = 4475.028| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4944 Z= 0.144 Angle : 0.623 6.807 6725 Z= 0.322 Chirality : 0.044 0.178 795 Planarity : 0.005 0.062 837 Dihedral : 4.221 21.352 686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % 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: -0.09 (0.34), residues: 633 helix: 1.63 (0.29), residues: 314 sheet: -1.51 (0.58), residues: 90 loop : -1.87 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.002 0.001 HIS B 31 PHE 0.017 0.002 PHE C 50 TYR 0.020 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 267) hydrogen bonds : angle 4.36983 ( 771) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.32660 ( 4) covalent geometry : bond 0.00333 ( 4942) covalent geometry : angle 0.62337 ( 6721) ********************** 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 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.7475 (ptp) cc_final: 0.7200 (ptm) REVERT: A 385 ILE cc_start: 0.7871 (tp) cc_final: 0.7644 (tp) REVERT: C 14 PRO cc_start: 0.8760 (Cg_exo) cc_final: 0.8434 (Cg_endo) REVERT: C 30 MET cc_start: 0.8613 (pmm) cc_final: 0.6847 (ptm) REVERT: C 58 ASN cc_start: 0.8795 (p0) cc_final: 0.8104 (p0) REVERT: B 47 PHE cc_start: 0.8670 (t80) cc_final: 0.8420 (t80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1856 time to fit residues: 36.2151 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 : 0.907 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.162679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.134868 restraints weight = 7159.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.134335 restraints weight = 6086.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135100 restraints weight = 6037.315| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4944 Z= 0.138 Angle : 0.637 7.799 6725 Z= 0.328 Chirality : 0.044 0.179 795 Planarity : 0.005 0.061 837 Dihedral : 4.238 21.005 686 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % 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: -0.05 (0.34), residues: 633 helix: 1.62 (0.29), residues: 314 sheet: -1.54 (0.60), residues: 84 loop : -1.76 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.001 0.001 HIS B 31 PHE 0.020 0.002 PHE C 50 TYR 0.021 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 267) hydrogen bonds : angle 4.37810 ( 771) SS BOND : bond 0.00212 ( 2) SS BOND : angle 0.37702 ( 4) covalent geometry : bond 0.00320 ( 4942) covalent geometry : angle 0.63735 ( 6721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2525.72 seconds wall clock time: 46 minutes 37.41 seconds (2797.41 seconds total)