Starting phenix.real_space_refine on Sat May 10 05:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p71_17514/05_2025/8p71_17514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p71_17514/05_2025/8p71_17514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p71_17514/05_2025/8p71_17514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p71_17514/05_2025/8p71_17514.map" model { file = "/net/cci-nas-00/data/ceres_data/8p71_17514/05_2025/8p71_17514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p71_17514/05_2025/8p71_17514.cif" } resolution = 2.0 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= 0.001 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 31 5.16 5 C 3289 2.51 5 N 870 2.21 5 O 1027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5217 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'X4F': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 4.63, per 1000 atoms: 0.89 Number of scatterers: 5217 At special positions: 0 Unit cell: (84.7875, 94.05, 67.6875, 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 31 16.00 O 1027 8.00 N 870 7.00 C 3289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.44 Conformation dependent library (CDL) restraints added in 565.3 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 271 through 275 removed outlier: 3.587A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.850A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.853A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.554A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.626A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 removed outlier: 3.772A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.543A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.897A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.766A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.262A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.738A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 6.616A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 271 hydrogen bonds defined for protein. 765 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: 1.29 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: 1642 1.34 - 1.46: 1189 1.46 - 1.58: 2346 1.58 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C08 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 1.342 1.491 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C02 X4F J 401 " pdb=" C04 X4F J 401 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C18 X4F J 401 " pdb=" N19 X4F J 401 " ideal model delta sigma weight residual 1.365 1.454 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C10 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 1.451 1.510 -0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C27 X4F J 401 " pdb=" N26 X4F J 401 " ideal model delta sigma weight residual 1.344 1.395 -0.051 2.00e-02 2.50e+03 6.59e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 6885 1.41 - 2.82: 135 2.82 - 4.23: 45 4.23 - 5.64: 8 5.64 - 7.04: 2 Bond angle restraints: 7075 Sorted by residual: angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 119.74 -7.04 3.00e+00 1.11e-01 5.51e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.96 3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" C04 X4F J 401 " pdb=" C05 X4F J 401 " pdb=" N06 X4F J 401 " ideal model delta sigma weight residual 113.81 107.42 6.39 3.00e+00 1.11e-01 4.54e+00 angle pdb=" CB GLU H 262 " pdb=" CG GLU H 262 " pdb=" CD GLU H 262 " ideal model delta sigma weight residual 112.60 116.04 -3.44 1.70e+00 3.46e-01 4.09e+00 angle pdb=" C17 X4F J 401 " pdb=" C08 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 126.29 120.82 5.47 3.00e+00 1.11e-01 3.32e+00 ... (remaining 7070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2695 16.15 - 32.31: 325 32.31 - 48.46: 99 48.46 - 64.61: 35 64.61 - 80.76: 12 Dihedral angle restraints: 3166 sinusoidal: 1319 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR I 176 " pdb=" C THR I 176 " pdb=" N ARG I 177 " pdb=" CA ARG I 177 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLN H 281 " pdb=" CB GLN H 281 " pdb=" CG GLN H 281 " pdb=" CD GLN H 281 " ideal model delta sinusoidal sigma weight residual 60.00 119.99 -59.99 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 448 0.026 - 0.052: 192 0.052 - 0.077: 83 0.077 - 0.103: 40 0.103 - 0.129: 14 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE J 255 " pdb=" N ILE J 255 " pdb=" C ILE J 255 " pdb=" CB ILE J 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO J 140 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 210 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO J 211 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO J 211 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO J 211 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO I 50 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.015 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 870 2.76 - 3.29: 5174 3.29 - 3.83: 9865 3.83 - 4.36: 11471 4.36 - 4.90: 19039 Nonbonded interactions: 46419 Sorted by model distance: nonbonded pdb=" O HOH J 503 " pdb=" O HOH J 551 " model vdw 2.223 3.040 nonbonded pdb=" O TRP I 11 " pdb=" O HOH I 401 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP J 92 " pdb=" O HOH J 501 " model vdw 2.233 3.040 nonbonded pdb=" O HOH J 536 " pdb=" O HOH J 554 " model vdw 2.257 3.040 nonbonded pdb=" O HOH J 502 " pdb=" O HOH J 552 " model vdw 2.258 3.040 ... (remaining 46414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.004 0.149 5227 Z= 0.206 Angle : 0.549 7.044 7075 Z= 0.265 Chirality : 0.039 0.129 777 Planarity : 0.004 0.030 903 Dihedral : 16.922 80.763 1970 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 20.04 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.72 (0.34), residues: 618 helix: 1.89 (0.28), residues: 346 sheet: -0.80 (1.11), residues: 20 loop : 0.37 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.002 0.001 HIS J 258 PHE 0.014 0.002 PHE J 91 TYR 0.014 0.001 TYR I 2 ARG 0.003 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.12377 ( 271) hydrogen bonds : angle 5.79837 ( 765) covalent geometry : bond 0.00423 ( 5227) covalent geometry : angle 0.54936 ( 7075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.599 Fit side-chains REVERT: I 232 LEU cc_start: 0.8173 (mm) cc_final: 0.7884 (mm) REVERT: J 252 PHE cc_start: 0.6732 (m-80) cc_final: 0.6433 (m-10) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 1.5662 time to fit residues: 152.2145 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.180987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158463 restraints weight = 4643.544| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 0.99 r_work: 0.3820 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5227 Z= 0.103 Angle : 0.487 5.148 7075 Z= 0.249 Chirality : 0.039 0.125 777 Planarity : 0.004 0.034 903 Dihedral : 5.385 59.664 713 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.53 % Allowed : 18.05 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 2.03 (0.34), residues: 618 helix: 2.06 (0.28), residues: 351 sheet: 0.42 (1.22), residues: 16 loop : 0.49 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.013 0.001 PHE I 110 TYR 0.015 0.001 TYR I 91 ARG 0.002 0.000 ARG H 295 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 271) hydrogen bonds : angle 4.52866 ( 765) covalent geometry : bond 0.00212 ( 5227) covalent geometry : angle 0.48674 ( 7075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.555 Fit side-chains REVERT: I 232 LEU cc_start: 0.8064 (mm) cc_final: 0.7763 (mm) REVERT: J 252 PHE cc_start: 0.6706 (m-80) cc_final: 0.6363 (m-10) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 1.4155 time to fit residues: 152.2549 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.175069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152195 restraints weight = 4647.354| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 0.97 r_work: 0.3744 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5227 Z= 0.290 Angle : 0.703 7.543 7075 Z= 0.365 Chirality : 0.047 0.141 777 Planarity : 0.006 0.047 903 Dihedral : 6.048 57.972 709 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 15.88 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.09 (0.33), residues: 618 helix: 1.37 (0.27), residues: 350 sheet: -0.83 (0.92), residues: 30 loop : 0.10 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP J 132 HIS 0.006 0.002 HIS H 294 PHE 0.023 0.003 PHE J 91 TYR 0.025 0.003 TYR I 2 ARG 0.007 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.06095 ( 271) hydrogen bonds : angle 4.98019 ( 765) covalent geometry : bond 0.00641 ( 5227) covalent geometry : angle 0.70323 ( 7075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.630 Fit side-chains REVERT: H 295 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7414 (ttt-90) REVERT: I 63 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7285 (mmm160) REVERT: I 85 MET cc_start: 0.7824 (tpp) cc_final: 0.7489 (tpp) REVERT: J 188 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5697 (mmp80) outliers start: 17 outliers final: 10 residues processed: 104 average time/residue: 1.5065 time to fit residues: 162.2026 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 GLN I 18 GLN I 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.178706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155680 restraints weight = 4748.998| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.01 r_work: 0.3785 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5227 Z= 0.128 Angle : 0.529 5.072 7075 Z= 0.271 Chirality : 0.040 0.134 777 Planarity : 0.004 0.034 903 Dihedral : 5.255 59.214 709 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 16.61 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.73 (0.34), residues: 618 helix: 1.83 (0.28), residues: 351 sheet: 0.92 (1.26), residues: 15 loop : 0.28 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 2 ARG 0.003 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 271) hydrogen bonds : angle 4.50662 ( 765) covalent geometry : bond 0.00277 ( 5227) covalent geometry : angle 0.52859 ( 7075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.623 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 1.4216 time to fit residues: 145.8419 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 41 optimal weight: 0.3980 chunk 9 optimal weight: 6.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155205 restraints weight = 4636.799| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 0.99 r_work: 0.3779 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5227 Z= 0.148 Angle : 0.545 5.683 7075 Z= 0.280 Chirality : 0.041 0.132 777 Planarity : 0.004 0.034 903 Dihedral : 5.210 59.909 709 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 17.51 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.79 (0.34), residues: 618 helix: 1.90 (0.28), residues: 348 sheet: 0.95 (1.30), residues: 15 loop : 0.30 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.016 0.002 PHE J 91 TYR 0.018 0.002 TYR I 2 ARG 0.003 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 271) hydrogen bonds : angle 4.50810 ( 765) covalent geometry : bond 0.00322 ( 5227) covalent geometry : angle 0.54457 ( 7075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.616 Fit side-chains REVERT: H 295 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7381 (ttt-90) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 1.5001 time to fit residues: 158.2335 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.179130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.156347 restraints weight = 4654.470| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 0.99 r_work: 0.3792 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5227 Z= 0.126 Angle : 0.526 6.165 7075 Z= 0.267 Chirality : 0.040 0.130 777 Planarity : 0.004 0.034 903 Dihedral : 4.946 59.870 709 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.35 % Allowed : 17.69 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.94 (0.34), residues: 618 helix: 2.04 (0.28), residues: 348 sheet: 0.79 (1.25), residues: 15 loop : 0.35 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.015 0.001 TYR I 2 ARG 0.003 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 271) hydrogen bonds : angle 4.39928 ( 765) covalent geometry : bond 0.00273 ( 5227) covalent geometry : angle 0.52619 ( 7075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.640 Fit side-chains REVERT: I 85 MET cc_start: 0.7780 (tpp) cc_final: 0.7550 (tpp) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 1.4436 time to fit residues: 142.2040 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156664 restraints weight = 4627.935| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 0.99 r_work: 0.3796 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5227 Z= 0.122 Angle : 0.526 7.339 7075 Z= 0.266 Chirality : 0.040 0.129 777 Planarity : 0.004 0.035 903 Dihedral : 4.876 59.908 708 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 18.23 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.97 (0.34), residues: 618 helix: 2.08 (0.28), residues: 348 sheet: 0.81 (1.24), residues: 15 loop : 0.36 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.015 0.002 TYR I 2 ARG 0.003 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 271) hydrogen bonds : angle 4.35576 ( 765) covalent geometry : bond 0.00265 ( 5227) covalent geometry : angle 0.52602 ( 7075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.603 Fit side-chains REVERT: H 295 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7385 (ttt-90) REVERT: I 63 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7274 (mmm160) REVERT: I 85 MET cc_start: 0.7780 (tpp) cc_final: 0.7557 (tpp) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 1.5273 time to fit residues: 153.0938 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.180009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.157285 restraints weight = 4665.636| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.00 r_work: 0.3803 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5227 Z= 0.117 Angle : 0.525 8.044 7075 Z= 0.265 Chirality : 0.040 0.129 777 Planarity : 0.004 0.035 903 Dihedral : 4.829 59.947 708 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 19.68 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 2.00 (0.34), residues: 618 helix: 2.12 (0.28), residues: 348 sheet: 0.41 (1.23), residues: 16 loop : 0.36 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.015 0.001 TYR I 2 ARG 0.003 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 271) hydrogen bonds : angle 4.31309 ( 765) covalent geometry : bond 0.00255 ( 5227) covalent geometry : angle 0.52456 ( 7075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.664 Fit side-chains REVERT: I 85 MET cc_start: 0.7791 (tpp) cc_final: 0.7551 (tpp) outliers start: 10 outliers final: 9 residues processed: 94 average time/residue: 1.5255 time to fit residues: 148.3468 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.153667 restraints weight = 4680.141| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 0.99 r_work: 0.3759 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5227 Z= 0.218 Angle : 0.649 9.323 7075 Z= 0.331 Chirality : 0.044 0.136 777 Planarity : 0.005 0.036 903 Dihedral : 5.241 58.174 708 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 18.77 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.46 (0.34), residues: 618 helix: 1.64 (0.27), residues: 347 sheet: 0.95 (1.31), residues: 15 loop : 0.13 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 177 HIS 0.004 0.001 HIS J 131 PHE 0.021 0.003 PHE J 91 TYR 0.022 0.003 TYR I 2 ARG 0.004 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.05335 ( 271) hydrogen bonds : angle 4.68570 ( 765) covalent geometry : bond 0.00483 ( 5227) covalent geometry : angle 0.64904 ( 7075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.666 Fit side-chains REVERT: H 295 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7368 (ttt-90) REVERT: I 63 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7296 (mmm160) REVERT: I 85 MET cc_start: 0.7792 (tpp) cc_final: 0.7536 (tpp) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 1.5701 time to fit residues: 157.6673 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 0.0370 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 GLN I 18 GLN I 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.179398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156635 restraints weight = 4682.778| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.00 r_work: 0.3796 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5227 Z= 0.126 Angle : 0.554 8.925 7075 Z= 0.279 Chirality : 0.041 0.133 777 Planarity : 0.004 0.034 903 Dihedral : 4.937 59.540 708 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 18.59 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.86 (0.34), residues: 618 helix: 1.98 (0.28), residues: 348 sheet: 0.82 (1.23), residues: 15 loop : 0.30 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS I 100 PHE 0.014 0.002 PHE I 110 TYR 0.015 0.002 TYR I 2 ARG 0.003 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 271) hydrogen bonds : angle 4.41907 ( 765) covalent geometry : bond 0.00277 ( 5227) covalent geometry : angle 0.55366 ( 7075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.628 Fit side-chains REVERT: I 63 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7307 (mmm160) REVERT: I 85 MET cc_start: 0.7806 (tpp) cc_final: 0.7548 (tpp) REVERT: J 227 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6504 (mt-10) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 1.5309 time to fit residues: 153.7401 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.0050 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.180519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.157995 restraints weight = 4667.020| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 0.99 r_work: 0.3814 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5227 Z= 0.113 Angle : 0.534 8.716 7075 Z= 0.268 Chirality : 0.040 0.130 777 Planarity : 0.004 0.035 903 Dihedral : 4.830 59.515 708 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.99 % Allowed : 19.31 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 2.03 (0.35), residues: 618 helix: 2.13 (0.28), residues: 348 sheet: 0.33 (1.22), residues: 16 loop : 0.39 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS J 258 PHE 0.015 0.002 PHE I 110 TYR 0.015 0.002 TYR J 27 ARG 0.005 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 271) hydrogen bonds : angle 4.28059 ( 765) covalent geometry : bond 0.00246 ( 5227) covalent geometry : angle 0.53393 ( 7075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5517.58 seconds wall clock time: 95 minutes 35.43 seconds (5735.43 seconds total)