Starting phenix.real_space_refine on Thu Mar 6 07:12:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p70_17513/03_2025/8p70_17513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p70_17513/03_2025/8p70_17513.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/8p70_17513/03_2025/8p70_17513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p70_17513/03_2025/8p70_17513.map" model { file = "/net/cci-nas-00/data/ceres_data/8p70_17513/03_2025/8p70_17513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p70_17513/03_2025/8p70_17513.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 3309 2.51 5 N 876 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5282 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: 52 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 26 Unusual residues: {'X4Q': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 26 Unusual residues: {'X4Q': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01AX4Q J 401 " occ=0.81 ... (50 atoms not shown) pdb=" N25BX4Q J 401 " occ=0.19 Time building chain proxies: 4.27, per 1000 atoms: 0.81 Number of scatterers: 5282 At special positions: 0 Unit cell: (84.7875, 93.3375, 66.975, 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 1066 8.00 N 876 7.00 C 3309 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: 1.28 Conformation dependent library (CDL) restraints added in 668.6 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: 35 helices and 3 sheets defined 62.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'H' and resid 263 through 267 removed outlier: 3.514A pdb=" N LEU H 266 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 263 through 267' Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.537A 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: 3.834A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 removed outlier: 3.621A pdb=" N ASN I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.543A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.982A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.794A 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: 4.622A 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 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.649A 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: 4.419A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 removed outlier: 3.869A pdb=" N ILE I 251 " --> pdb=" O GLN I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 67 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: 4.366A 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 removed outlier: 3.514A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) 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 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.707A 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: 6.552A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.864A 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 134 272 hydrogen bonds defined for protein. 762 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: 1.46 Time building geometry restraints manager: 1.52 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: 1644 1.34 - 1.46: 1122 1.46 - 1.58: 2438 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5255 Sorted by residual: bond pdb=" C15BX4Q J 401 " pdb=" N16BX4Q J 401 " ideal model delta sigma weight residual 1.357 1.491 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C15AX4Q J 401 " pdb=" N16AX4Q J 401 " ideal model delta sigma weight residual 1.357 1.491 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C02BX4Q J 401 " pdb=" C04BX4Q J 401 " ideal model delta sigma weight residual 1.496 1.598 -0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C02AX4Q J 401 " pdb=" C04AX4Q J 401 " ideal model delta sigma weight residual 1.496 1.598 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C07AX4Q J 401 " pdb=" N08AX4Q J 401 " ideal model delta sigma weight residual 1.367 1.453 -0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 5250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 6917 1.52 - 3.05: 141 3.05 - 4.57: 39 4.57 - 6.10: 10 6.10 - 7.62: 6 Bond angle restraints: 7113 Sorted by residual: angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" N MET I 237 " pdb=" CA MET I 237 " pdb=" CB MET I 237 " ideal model delta sigma weight residual 113.65 109.48 4.17 1.47e+00 4.63e-01 8.06e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.27 4.63 1.80e+00 3.09e-01 6.63e+00 angle pdb=" CB MET I 75 " pdb=" CG MET I 75 " pdb=" SD MET I 75 " ideal model delta sigma weight residual 112.70 106.11 6.59 3.00e+00 1.11e-01 4.83e+00 angle pdb=" C PHE I 90 " pdb=" N TYR I 91 " pdb=" CA TYR I 91 " ideal model delta sigma weight residual 122.56 118.83 3.73 1.72e+00 3.38e-01 4.69e+00 ... (remaining 7108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 2879 22.38 - 44.77: 252 44.77 - 67.15: 35 67.15 - 89.53: 11 89.53 - 111.92: 2 Dihedral angle restraints: 3179 sinusoidal: 1332 harmonic: 1847 Sorted by residual: dihedral pdb=" C07BX4Q J 401 " pdb=" C09BX4Q J 401 " pdb=" N08BX4Q J 401 " pdb=" C10BX4Q J 401 " ideal model delta sinusoidal sigma weight residual 291.54 179.62 111.92 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C07BX4Q J 401 " pdb=" C09BX4Q J 401 " pdb=" N08BX4Q J 401 " pdb=" C13BX4Q J 401 " ideal model delta sinusoidal sigma weight residual 174.58 62.87 111.71 1 3.00e+01 1.11e-03 1.46e+01 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 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 472 0.029 - 0.058: 198 0.058 - 0.087: 59 0.087 - 0.116: 37 0.116 - 0.145: 11 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 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA PRO J 140 " pdb=" N PRO J 140 " pdb=" C PRO J 140 " pdb=" CB PRO J 140 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 774 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 237 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET I 237 " 0.030 2.00e-02 2.50e+03 pdb=" O MET I 237 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU I 238 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO I 50 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO J 140 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.021 5.00e-02 4.00e+02 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 529 2.74 - 3.28: 5489 3.28 - 3.82: 10018 3.82 - 4.36: 11931 4.36 - 4.90: 19411 Nonbonded interactions: 47378 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.202 3.040 nonbonded pdb=" O ARG I 9 " pdb=" O HOH I 401 " model vdw 2.208 3.040 nonbonded pdb=" O LEU I 144 " pdb=" O HOH I 402 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP J 104 " pdb=" OG SER J 106 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.235 3.040 ... (remaining 47373 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=0.19 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.180 Find NCS groups from input model: 0.080 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:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.006 0.134 5255 Z= 0.378 Angle : 0.617 7.621 7113 Z= 0.297 Chirality : 0.040 0.145 777 Planarity : 0.005 0.041 905 Dihedral : 16.718 111.917 1983 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 16.43 % Favored : 82.67 % 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: 1.67 (0.34), residues: 618 helix: 1.97 (0.29), residues: 334 sheet: 0.84 (1.05), residues: 15 loop : 0.08 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 231 ARG 0.006 0.000 ARG I 63 *********************** 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 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.580 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 1.4771 time to fit residues: 145.3554 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.170519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142892 restraints weight = 19552.760| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.48 r_work: 0.3620 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5255 Z= 0.189 Angle : 0.534 6.407 7113 Z= 0.278 Chirality : 0.040 0.139 777 Planarity : 0.005 0.041 905 Dihedral : 7.326 92.203 725 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 14.62 % Favored : 83.75 % 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: 1.83 (0.34), residues: 618 helix: 2.04 (0.29), residues: 345 sheet: 0.72 (1.08), residues: 15 loop : 0.18 (0.39), residues: 258 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 I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.549 Fit side-chains REVERT: I 189 LYS cc_start: 0.7477 (mmmm) cc_final: 0.7271 (mptm) REVERT: J 246 TYR cc_start: 0.6762 (t80) cc_final: 0.6525 (t80) outliers start: 9 outliers final: 3 residues processed: 102 average time/residue: 1.4509 time to fit residues: 153.2338 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 93 ASN J 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.171468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.144079 restraints weight = 18171.990| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.40 r_work: 0.3636 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5255 Z= 0.163 Angle : 0.527 8.649 7113 Z= 0.268 Chirality : 0.039 0.138 777 Planarity : 0.005 0.039 905 Dihedral : 6.176 58.261 722 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.17 % Allowed : 15.70 % Favored : 82.13 % 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: 1.91 (0.34), residues: 618 helix: 2.13 (0.28), residues: 345 sheet: 0.54 (1.07), residues: 15 loop : 0.18 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.001 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.005 0.000 ARG I 63 *********************** 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 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.612 Fit side-chains REVERT: I 260 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6925 (ttmt) REVERT: J 246 TYR cc_start: 0.6744 (t80) cc_final: 0.6486 (t80) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 1.5740 time to fit residues: 175.8136 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 266 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.168384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141094 restraints weight = 16946.956| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.26 r_work: 0.3607 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5255 Z= 0.286 Angle : 0.616 7.208 7113 Z= 0.315 Chirality : 0.043 0.149 777 Planarity : 0.005 0.044 905 Dihedral : 6.761 67.392 722 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.35 % Allowed : 14.62 % Favored : 83.03 % 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: 1.57 (0.34), residues: 618 helix: 1.82 (0.28), residues: 343 sheet: 0.55 (1.18), residues: 15 loop : 0.10 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.005 0.001 ARG I 23 *********************** 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: 13 poor density : 94 time to evaluate : 0.619 Fit side-chains REVERT: I 250 ASP cc_start: 0.7398 (p0) cc_final: 0.7059 (m-30) REVERT: I 260 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6877 (ttmt) outliers start: 13 outliers final: 4 residues processed: 103 average time/residue: 1.5038 time to fit residues: 160.2949 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.170884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143484 restraints weight = 16432.199| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.11 r_work: 0.3645 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5255 Z= 0.172 Angle : 0.526 6.555 7113 Z= 0.271 Chirality : 0.040 0.141 777 Planarity : 0.005 0.042 905 Dihedral : 5.823 53.637 722 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 16.25 % Favored : 82.13 % 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: 1.87 (0.34), residues: 618 helix: 2.13 (0.28), residues: 344 sheet: 0.41 (1.15), residues: 15 loop : 0.13 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.006 0.000 ARG I 63 *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.624 Fit side-chains REVERT: I 77 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6211 (ptp-170) REVERT: I 260 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6888 (ttmt) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 1.4989 time to fit residues: 156.9112 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.169250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141066 restraints weight = 21113.472| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.58 r_work: 0.3598 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5255 Z= 0.232 Angle : 0.573 6.090 7113 Z= 0.294 Chirality : 0.041 0.146 777 Planarity : 0.005 0.043 905 Dihedral : 6.185 58.964 722 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 16.06 % Favored : 82.13 % 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: 1.95 (0.28), residues: 344 sheet: 0.49 (1.20), residues: 15 loop : 0.17 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.005 0.000 ARG I 63 *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.573 Fit side-chains REVERT: I 77 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6335 (ptp-170) REVERT: I 250 ASP cc_start: 0.7388 (p0) cc_final: 0.7003 (m-30) REVERT: I 260 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6889 (ttmt) REVERT: J 227 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6779 (pt0) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 1.5583 time to fit residues: 161.1881 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.170005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142558 restraints weight = 16454.250| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.11 r_work: 0.3634 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5255 Z= 0.199 Angle : 0.564 9.886 7113 Z= 0.286 Chirality : 0.040 0.145 777 Planarity : 0.005 0.043 905 Dihedral : 5.875 54.787 722 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 16.25 % Favored : 82.31 % 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: 2.02 (0.28), residues: 345 sheet: 0.41 (1.18), residues: 15 loop : 0.16 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.000 ARG I 63 *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.617 Fit side-chains REVERT: I 77 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6251 (ptp-170) REVERT: I 260 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6817 (ttmt) REVERT: J 227 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6777 (pt0) outliers start: 8 outliers final: 4 residues processed: 98 average time/residue: 1.5792 time to fit residues: 160.1953 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 0.0470 chunk 51 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.172203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143959 restraints weight = 22243.754| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.66 r_work: 0.3636 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 5255 Z= 0.151 Angle : 0.522 8.969 7113 Z= 0.265 Chirality : 0.039 0.141 777 Planarity : 0.005 0.042 905 Dihedral : 5.421 52.141 722 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 16.79 % Favored : 81.59 % 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: 2.01 (0.34), residues: 618 helix: 2.27 (0.29), residues: 344 sheet: 0.43 (1.15), residues: 15 loop : 0.16 (0.39), residues: 259 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 0.013 0.001 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.006 0.000 ARG I 63 *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.651 Fit side-chains REVERT: I 77 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6244 (ptp-170) REVERT: I 260 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6872 (ttmt) REVERT: J 227 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6775 (pt0) outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 1.6067 time to fit residues: 164.6253 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 266 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 chunk 1 optimal weight: 0.0070 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.172153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145371 restraints weight = 19274.027| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.35 r_work: 0.3653 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5255 Z= 0.150 Angle : 0.526 8.643 7113 Z= 0.265 Chirality : 0.039 0.139 777 Planarity : 0.005 0.041 905 Dihedral : 5.332 53.586 722 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 17.51 % Favored : 81.59 % 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: 2.06 (0.34), residues: 618 helix: 2.31 (0.28), residues: 344 sheet: 0.51 (1.15), residues: 15 loop : 0.17 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.013 0.001 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.007 0.000 ARG I 63 *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.547 Fit side-chains REVERT: I 77 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6198 (ptp-170) REVERT: I 228 MET cc_start: 0.8074 (ptm) cc_final: 0.7785 (ptm) REVERT: I 260 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6908 (ttmt) REVERT: J 227 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6724 (pt0) outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 1.4452 time to fit residues: 145.1735 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 : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.170490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143182 restraints weight = 22095.375| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.51 r_work: 0.3624 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5255 Z= 0.184 Angle : 0.556 8.416 7113 Z= 0.281 Chirality : 0.040 0.139 777 Planarity : 0.005 0.041 905 Dihedral : 5.537 56.794 722 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 17.51 % Favored : 81.41 % 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: 1.95 (0.34), residues: 618 helix: 2.21 (0.28), residues: 344 sheet: 0.51 (1.15), residues: 15 loop : 0.15 (0.39), residues: 259 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 I 30 TYR 0.019 0.002 TYR I 91 ARG 0.007 0.000 ARG I 63 ********************** 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.630 Fit side-chains REVERT: I 77 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6260 (ptp-170) REVERT: I 260 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6862 (ttmt) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.5909 time to fit residues: 153.4487 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 266 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.171226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144033 restraints weight = 21597.473| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.48 r_work: 0.3633 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5255 Z= 0.166 Angle : 0.546 8.274 7113 Z= 0.276 Chirality : 0.040 0.138 777 Planarity : 0.005 0.041 905 Dihedral : 5.387 52.997 722 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 17.69 % Favored : 81.23 % 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: 2.26 (0.28), residues: 344 sheet: 0.48 (1.13), residues: 15 loop : 0.17 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.001 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.007 0.000 ARG I 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6795.25 seconds wall clock time: 115 minutes 55.60 seconds (6955.60 seconds total)