Starting phenix.real_space_refine on Mon Jan 13 19:38:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w22_43737/01_2025/8w22_43737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w22_43737/01_2025/8w22_43737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w22_43737/01_2025/8w22_43737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w22_43737/01_2025/8w22_43737.map" model { file = "/net/cci-nas-00/data/ceres_data/8w22_43737/01_2025/8w22_43737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w22_43737/01_2025/8w22_43737.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2333 2.51 5 N 723 2.21 5 O 681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3750 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 685 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 805 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 117} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2260 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 798 Unresolved non-hydrogen angles: 1047 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 37, 'TYR:plan': 7, 'ASN:plan1': 18, 'TRP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 428 Time building chain proxies: 3.14, per 1000 atoms: 0.84 Number of scatterers: 3750 At special positions: 0 Unit cell: (69.126, 131.508, 116.334, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 681 8.00 N 723 7.00 C 2333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 96 " distance=2.05 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 71 " distance=2.08 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 713.4 milliseconds 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 19.4% alpha, 26.4% 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 99 through 111 removed outlier: 3.577A pdb=" N MET A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.959A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 136 through 139 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.504A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 238 through 247 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.711A pdb=" N CYS B 96 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.525A pdb=" N ALA B 104 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 126 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 162 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 124 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.536A pdb=" N GLU C 112 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR C 91 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 7.338A pdb=" N ARG C 137 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLY C 212 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 233 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER C 217 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 231 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR C 184 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL C 173 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASP C 203 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL C 152 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 212 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN C 202 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU C 210 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS C 204 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AA6, first strand: chain 'C' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 369 Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.529A pdb=" N THR C 411 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR C 425 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 486 173 hydrogen bonds defined for protein. 453 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: 1.09 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1142 1.33 - 1.45: 504 1.45 - 1.58: 2130 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3796 Sorted by residual: bond pdb=" NE ARG A 106 " pdb=" CZ ARG A 106 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 6.76e+00 bond pdb=" NE ARG C 119 " pdb=" CZ ARG C 119 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.10e-02 8.26e+03 6.04e+00 bond pdb=" NE ARG A 162 " pdb=" CZ ARG A 162 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.31e+00 bond pdb=" NE ARG C 97 " pdb=" CZ ARG C 97 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.20e+00 bond pdb=" NE ARG A 124 " pdb=" CZ ARG A 124 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.05e+00 ... (remaining 3791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 4429 1.58 - 3.16: 651 3.16 - 4.75: 60 4.75 - 6.33: 27 6.33 - 7.91: 28 Bond angle restraints: 5195 Sorted by residual: angle pdb=" C VAL C 114 " pdb=" N PRO C 115 " pdb=" CA PRO C 115 " ideal model delta sigma weight residual 119.85 127.71 -7.86 1.01e+00 9.80e-01 6.05e+01 angle pdb=" C ASP B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta sigma weight residual 119.76 126.92 -7.16 1.03e+00 9.43e-01 4.84e+01 angle pdb=" C ARG C 502 " pdb=" N PRO C 503 " pdb=" CA PRO C 503 " ideal model delta sigma weight residual 120.03 126.91 -6.88 9.90e-01 1.02e+00 4.83e+01 angle pdb=" C GLY A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta sigma weight residual 119.32 127.23 -7.91 1.14e+00 7.69e-01 4.81e+01 angle pdb=" C MET B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta sigma weight residual 120.31 127.11 -6.80 9.80e-01 1.04e+00 4.81e+01 ... (remaining 5190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.31: 2128 12.31 - 24.61: 57 24.61 - 36.92: 16 36.92 - 49.23: 6 49.23 - 61.53: 6 Dihedral angle restraints: 2213 sinusoidal: 467 harmonic: 1746 Sorted by residual: dihedral pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " pdb=" SG CYS C 222 " pdb=" CB CYS C 222 " ideal model delta sinusoidal sigma weight residual 93.00 154.53 -61.53 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 71 " pdb=" CB CYS C 71 " ideal model delta sinusoidal sigma weight residual 93.00 137.06 -44.06 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 120.80 -27.80 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 2210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 349 0.039 - 0.079: 170 0.079 - 0.118: 73 0.118 - 0.157: 24 0.157 - 0.197: 3 Chirality restraints: 619 Sorted by residual: chirality pdb=" CA ILE C 191 " pdb=" N ILE C 191 " pdb=" C ILE C 191 " pdb=" CB ILE C 191 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ILE C 130 " pdb=" N ILE C 130 " pdb=" C ILE C 130 " pdb=" CB ILE C 130 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU C 46 " pdb=" CB LEU C 46 " pdb=" CD1 LEU C 46 " pdb=" CD2 LEU C 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 616 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 52 " -0.028 2.00e-02 2.50e+03 1.43e-02 4.08e+00 pdb=" CG TYR B 52 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 52 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 52 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 52 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 52 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 52 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 199 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C PRO C 199 " 0.032 2.00e-02 2.50e+03 pdb=" O PRO C 199 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 200 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 52 " 0.021 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR C 52 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 52 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 52 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 52 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 52 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 52 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 52 " 0.015 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1763 2.98 - 3.46: 3227 3.46 - 3.94: 5318 3.94 - 4.42: 5604 4.42 - 4.90: 9568 Nonbonded interactions: 25480 Sorted by model distance: nonbonded pdb=" O TYR B 147 " pdb=" C GLY B 148 " model vdw 2.497 3.270 nonbonded pdb=" O TYR B 147 " pdb=" N ALA B 150 " model vdw 2.511 3.120 nonbonded pdb=" N GLY C 194 " pdb=" N ASP C 195 " model vdw 2.565 2.560 nonbonded pdb=" N LYS C 39 " pdb=" N LEU C 40 " model vdw 2.578 2.560 nonbonded pdb=" N GLY C 268 " pdb=" N ARG C 269 " model vdw 2.602 2.560 ... (remaining 25475 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: 1.250 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.008 0.050 3796 Z= 0.572 Angle : 1.266 7.910 5195 Z= 0.882 Chirality : 0.055 0.197 619 Planarity : 0.005 0.018 718 Dihedral : 7.997 59.354 1082 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.84 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.35), residues: 599 helix: -0.58 (0.43), residues: 110 sheet: 1.43 (0.46), residues: 140 loop : 0.03 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP C 64 HIS 0.004 0.001 HIS C 116 PHE 0.018 0.003 PHE C 171 TYR 0.028 0.004 TYR B 52 ARG 0.004 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.411 Fit side-chains REVERT: A 106 ARG cc_start: 0.6014 (ttm110) cc_final: 0.5118 (tpp-160) REVERT: A 170 GLN cc_start: 0.8282 (mt0) cc_final: 0.8030 (mt0) REVERT: B 100 MET cc_start: 0.8401 (mmm) cc_final: 0.7447 (mpp) REVERT: C 125 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7217 (tmt-80) REVERT: C 137 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7137 (mtp85) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2009 time to fit residues: 17.2751 Evaluate side-chains 41 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121210 restraints weight = 7309.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118813 restraints weight = 6787.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120223 restraints weight = 5301.348| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3796 Z= 0.292 Angle : 0.619 5.445 5195 Z= 0.339 Chirality : 0.047 0.163 619 Planarity : 0.005 0.028 718 Dihedral : 4.303 18.740 644 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.33 % Allowed : 14.44 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.83 (0.36), residues: 599 helix: 0.85 (0.49), residues: 115 sheet: 0.98 (0.42), residues: 169 loop : 0.31 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 117 HIS 0.002 0.001 HIS C 116 PHE 0.016 0.002 PHE C 171 TYR 0.017 0.002 TYR C 52 ARG 0.005 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.433 Fit side-chains REVERT: A 106 ARG cc_start: 0.5715 (ttm110) cc_final: 0.4888 (tpp-160) REVERT: A 156 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 100 MET cc_start: 0.9005 (mmm) cc_final: 0.8649 (mmt) REVERT: C 125 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7569 (tmt-80) REVERT: C 137 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7046 (mtp85) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.1376 time to fit residues: 8.7255 Evaluate side-chains 44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113530 restraints weight = 7357.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112310 restraints weight = 5793.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113286 restraints weight = 5073.877| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 3796 Z= 0.549 Angle : 0.790 7.780 5195 Z= 0.432 Chirality : 0.052 0.193 619 Planarity : 0.006 0.040 718 Dihedral : 5.539 21.045 644 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.00 % Allowed : 18.89 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.25 (0.35), residues: 599 helix: -0.17 (0.49), residues: 113 sheet: 0.58 (0.42), residues: 156 loop : -0.47 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP B 117 HIS 0.010 0.003 HIS B 72 PHE 0.020 0.004 PHE B 50 TYR 0.021 0.003 TYR A 185 ARG 0.006 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.392 Fit side-chains REVERT: C 125 ARG cc_start: 0.8152 (ttt180) cc_final: 0.7699 (ttt90) REVERT: C 137 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7482 (mtp85) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.1231 time to fit residues: 7.4932 Evaluate side-chains 39 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 0.0980 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 0.0060 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.149415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121834 restraints weight = 7142.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121178 restraints weight = 6101.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122522 restraints weight = 5811.061| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3796 Z= 0.179 Angle : 0.535 6.306 5195 Z= 0.282 Chirality : 0.045 0.134 619 Planarity : 0.004 0.036 718 Dihedral : 4.181 15.833 644 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.44 % Allowed : 18.33 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.10 (0.36), residues: 599 helix: 0.86 (0.54), residues: 109 sheet: 0.34 (0.42), residues: 162 loop : -0.28 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 117 HIS 0.003 0.001 HIS B 72 PHE 0.018 0.002 PHE C 171 TYR 0.007 0.001 TYR A 138 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.381 Fit side-chains REVERT: C 121 MET cc_start: 0.7839 (tpt) cc_final: 0.7301 (tpp) REVERT: C 125 ARG cc_start: 0.8013 (ttt180) cc_final: 0.7624 (ttt90) REVERT: C 137 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7381 (mtp85) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1169 time to fit residues: 7.6305 Evaluate side-chains 43 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 17 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118374 restraints weight = 7430.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117577 restraints weight = 5853.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118742 restraints weight = 5869.726| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3796 Z= 0.234 Angle : 0.541 6.677 5195 Z= 0.286 Chirality : 0.045 0.135 619 Planarity : 0.004 0.035 718 Dihedral : 3.992 16.687 644 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.56 % Allowed : 19.44 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.19 (0.37), residues: 599 helix: 0.98 (0.54), residues: 109 sheet: 0.47 (0.45), residues: 145 loop : -0.24 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 117 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.002 PHE C 171 TYR 0.008 0.001 TYR A 185 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.431 Fit side-chains REVERT: B 87 MET cc_start: 0.8186 (mtm) cc_final: 0.7953 (ptm) REVERT: C 121 MET cc_start: 0.7853 (tpt) cc_final: 0.7320 (tpp) REVERT: C 125 ARG cc_start: 0.8323 (ttt180) cc_final: 0.7901 (ttt90) REVERT: C 137 ARG cc_start: 0.8271 (mtp180) cc_final: 0.7427 (mtp85) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.1199 time to fit residues: 8.0001 Evaluate side-chains 45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119505 restraints weight = 7366.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118358 restraints weight = 6202.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119275 restraints weight = 4901.185| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3796 Z= 0.157 Angle : 0.496 6.974 5195 Z= 0.254 Chirality : 0.044 0.132 619 Planarity : 0.004 0.042 718 Dihedral : 3.575 14.450 644 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.89 % Allowed : 21.67 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.41 (0.37), residues: 599 helix: 1.24 (0.55), residues: 109 sheet: 0.33 (0.43), residues: 156 loop : 0.01 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 117 HIS 0.003 0.001 HIS A 146 PHE 0.018 0.002 PHE C 171 TYR 0.007 0.001 TYR A 138 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.404 Fit side-chains REVERT: C 121 MET cc_start: 0.7981 (tpt) cc_final: 0.7282 (tpp) REVERT: C 125 ARG cc_start: 0.8282 (ttt180) cc_final: 0.7868 (ttt90) REVERT: C 137 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7342 (mtp85) outliers start: 7 outliers final: 7 residues processed: 44 average time/residue: 0.1237 time to fit residues: 7.4625 Evaluate side-chains 42 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118192 restraints weight = 7296.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116961 restraints weight = 6204.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117621 restraints weight = 5073.894| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3796 Z= 0.198 Angle : 0.512 6.993 5195 Z= 0.265 Chirality : 0.044 0.132 619 Planarity : 0.004 0.040 718 Dihedral : 3.626 15.367 644 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.00 % Allowed : 19.44 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.25 (0.37), residues: 599 helix: 0.91 (0.54), residues: 115 sheet: 0.34 (0.45), residues: 137 loop : -0.07 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 117 HIS 0.003 0.001 HIS A 146 PHE 0.016 0.002 PHE C 171 TYR 0.005 0.001 TYR A 185 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.429 Fit side-chains REVERT: B 112 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: C 121 MET cc_start: 0.7991 (tpt) cc_final: 0.7306 (tpp) REVERT: C 125 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7803 (ttt90) REVERT: C 137 ARG cc_start: 0.8266 (mtp180) cc_final: 0.7374 (mtp85) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.1211 time to fit residues: 7.4554 Evaluate side-chains 41 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119184 restraints weight = 7437.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117950 restraints weight = 6455.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118745 restraints weight = 5300.981| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3796 Z= 0.166 Angle : 0.499 7.429 5195 Z= 0.257 Chirality : 0.044 0.131 619 Planarity : 0.003 0.042 718 Dihedral : 3.478 14.532 644 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.44 % Allowed : 21.11 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.39 (0.37), residues: 599 helix: 0.98 (0.54), residues: 115 sheet: 0.24 (0.44), residues: 148 loop : 0.13 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 117 HIS 0.003 0.001 HIS A 146 PHE 0.019 0.002 PHE C 171 TYR 0.006 0.001 TYR A 138 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.418 Fit side-chains REVERT: A 196 VAL cc_start: 0.7413 (p) cc_final: 0.7204 (p) REVERT: B 112 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: C 121 MET cc_start: 0.7968 (tpt) cc_final: 0.7310 (tpp) REVERT: C 125 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7799 (ttt90) REVERT: C 137 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7403 (mtp85) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.1213 time to fit residues: 7.4289 Evaluate side-chains 42 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.118914 restraints weight = 7293.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117776 restraints weight = 5661.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119028 restraints weight = 4932.176| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3796 Z= 0.177 Angle : 0.501 7.923 5195 Z= 0.257 Chirality : 0.044 0.131 619 Planarity : 0.003 0.044 718 Dihedral : 3.449 14.975 644 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.00 % Allowed : 19.44 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.33 (0.37), residues: 599 helix: 0.97 (0.54), residues: 115 sheet: 0.36 (0.45), residues: 137 loop : -0.01 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 117 HIS 0.003 0.001 HIS B 72 PHE 0.016 0.002 PHE C 171 TYR 0.004 0.001 TYR C 52 ARG 0.001 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.414 Fit side-chains REVERT: A 196 VAL cc_start: 0.6983 (p) cc_final: 0.6675 (p) REVERT: B 112 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: C 121 MET cc_start: 0.7953 (tpt) cc_final: 0.7325 (tpp) REVERT: C 125 ARG cc_start: 0.8115 (ttt180) cc_final: 0.7797 (ttt90) REVERT: C 137 ARG cc_start: 0.8325 (mtp180) cc_final: 0.7483 (mtp85) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.1140 time to fit residues: 7.2393 Evaluate side-chains 45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118057 restraints weight = 7464.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117459 restraints weight = 6321.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118898 restraints weight = 4831.117| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3796 Z= 0.198 Angle : 0.510 8.360 5195 Z= 0.263 Chirality : 0.044 0.132 619 Planarity : 0.004 0.043 718 Dihedral : 3.544 15.120 644 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.00 % Allowed : 20.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.27 (0.37), residues: 599 helix: 0.94 (0.54), residues: 115 sheet: 0.32 (0.44), residues: 141 loop : -0.06 (0.37), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 117 HIS 0.004 0.001 HIS A 146 PHE 0.017 0.002 PHE C 171 TYR 0.005 0.001 TYR A 138 ARG 0.002 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.382 Fit side-chains REVERT: A 196 VAL cc_start: 0.6871 (p) cc_final: 0.6559 (p) REVERT: B 112 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8535 (mp10) REVERT: C 121 MET cc_start: 0.7930 (tpt) cc_final: 0.7309 (tpp) REVERT: C 125 ARG cc_start: 0.8086 (ttt180) cc_final: 0.7799 (ttt90) REVERT: C 137 ARG cc_start: 0.8371 (mtp180) cc_final: 0.7538 (mtp85) outliers start: 9 outliers final: 8 residues processed: 44 average time/residue: 0.1244 time to fit residues: 7.3996 Evaluate side-chains 43 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.0470 chunk 20 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118409 restraints weight = 7381.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116349 restraints weight = 7058.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117988 restraints weight = 5323.558| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3796 Z= 0.171 Angle : 0.496 8.905 5195 Z= 0.252 Chirality : 0.044 0.130 619 Planarity : 0.003 0.045 718 Dihedral : 3.380 14.608 644 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.56 % Allowed : 20.00 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.37), residues: 599 helix: 0.95 (0.54), residues: 115 sheet: 0.30 (0.46), residues: 131 loop : 0.01 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 117 HIS 0.003 0.001 HIS B 72 PHE 0.017 0.002 PHE C 171 TYR 0.006 0.001 TYR A 138 ARG 0.001 0.000 ARG C 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.86 seconds wall clock time: 27 minutes 7.41 seconds (1627.41 seconds total)