Starting phenix.real_space_refine on Thu Feb 13 14:29:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tq2_41499/02_2025/8tq2_41499_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tq2_41499/02_2025/8tq2_41499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tq2_41499/02_2025/8tq2_41499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tq2_41499/02_2025/8tq2_41499.map" model { file = "/net/cci-nas-00/data/ceres_data/8tq2_41499/02_2025/8tq2_41499_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tq2_41499/02_2025/8tq2_41499_neut.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4357 atoms to isotropic. 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 36 5.16 5 C 3569 2.51 5 N 931 2.21 5 O 969 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-5592/modules/chem_data/mon_lib" Total number of atoms: 5505 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 639 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 8, 'TRANS': 73} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 120 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "A" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2561 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 294} Chain breaks: 5 Chain: "B" Number of atoms: 2185 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 261, 2178 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 261, 2178 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain breaks: 1 bond proxies already assigned to first conformer: 2226 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AVAL B 163 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 163 " occ=0.50 Time building chain proxies: 5.13, per 1000 atoms: 0.93 Number of scatterers: 5505 At special positions: 0 Unit cell: (81.3276, 101.659, 82.3977, 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 36 16.00 O 969 8.00 N 931 7.00 C 3569 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: 1.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1292 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 52.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 37 through 44 removed outlier: 3.546A pdb=" N LYS C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 Processing helix chain 'D' and resid 1619 through 1623 removed outlier: 3.693A pdb=" N VAL D1622 " --> pdb=" O ARG D1619 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D1623 " --> pdb=" O ASP D1620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1619 through 1623' Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.629A pdb=" N VAL A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.750A pdb=" N MET A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.714A pdb=" N HIS A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.949A pdb=" N HIS A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 removed outlier: 3.600A pdb=" N ALA A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.914A pdb=" N ILE B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 82 through 98 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.512A pdb=" N PHE B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 193 through 209 removed outlier: 3.535A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 removed outlier: 3.793A pdb=" N GLU B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.619A pdb=" N GLU B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N THR B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 6.584A pdb=" N LYS A 26 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS A 37 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL A 93 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A 92 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 86 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP A 94 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL A 84 " --> pdb=" O TRP A 94 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 96 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.430A pdb=" N MET A 160 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 168 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 230 hydrogen bonds defined for protein. 679 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: 1.20 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1743 1.35 - 1.46: 1291 1.46 - 1.58: 2552 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 5644 Sorted by residual: bond pdb=" C MET A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.03e-01 bond pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.99e-01 bond pdb=" CG GLU B 98 " pdb=" CD GLU B 98 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.59e-01 bond pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta sigma weight residual 1.528 1.541 -0.013 1.59e-02 3.96e+03 6.43e-01 bond pdb=" N PRO B 193 " pdb=" CA PRO B 193 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.31e-02 5.83e+03 6.20e-01 ... (remaining 5639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7458 1.53 - 3.05: 125 3.05 - 4.58: 32 4.58 - 6.10: 7 6.10 - 7.63: 3 Bond angle restraints: 7625 Sorted by residual: angle pdb=" CB MET B 250 " pdb=" CG MET B 250 " pdb=" SD MET B 250 " ideal model delta sigma weight residual 112.70 120.33 -7.63 3.00e+00 1.11e-01 6.47e+00 angle pdb=" CB MET B 86 " pdb=" CG MET B 86 " pdb=" SD MET B 86 " ideal model delta sigma weight residual 112.70 120.32 -7.62 3.00e+00 1.11e-01 6.46e+00 angle pdb=" CA MET A 174 " pdb=" CB MET A 174 " pdb=" CG MET A 174 " ideal model delta sigma weight residual 114.10 118.42 -4.32 2.00e+00 2.50e-01 4.67e+00 angle pdb=" C LEU A 69 " pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 121.94 117.69 4.25 2.00e+00 2.50e-01 4.52e+00 angle pdb=" C LYS C 15 " pdb=" N ARG C 16 " pdb=" CA ARG C 16 " ideal model delta sigma weight residual 120.58 123.32 -2.74 1.32e+00 5.74e-01 4.29e+00 ... (remaining 7620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 2991 16.18 - 32.35: 337 32.35 - 48.53: 71 48.53 - 64.70: 10 64.70 - 80.88: 7 Dihedral angle restraints: 3416 sinusoidal: 1431 harmonic: 1985 Sorted by residual: dihedral pdb=" CA ASP B 20 " pdb=" CB ASP B 20 " pdb=" CG ASP B 20 " pdb=" OD1 ASP B 20 " ideal model delta sinusoidal sigma weight residual -30.00 -81.65 51.65 1 2.00e+01 2.50e-03 9.11e+00 dihedral pdb=" CG ARG B 58 " pdb=" CD ARG B 58 " pdb=" NE ARG B 58 " pdb=" CZ ARG B 58 " ideal model delta sinusoidal sigma weight residual 180.00 139.55 40.45 2 1.50e+01 4.44e-03 8.98e+00 dihedral pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " pdb=" CD GLU A 101 " pdb=" OE1 GLU A 101 " ideal model delta sinusoidal sigma weight residual 0.00 80.88 -80.88 1 3.00e+01 1.11e-03 8.98e+00 ... (remaining 3413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 481 0.028 - 0.057: 204 0.057 - 0.085: 90 0.085 - 0.113: 47 0.113 - 0.141: 5 Chirality restraints: 827 Sorted by residual: chirality pdb=" CA VAL B 222 " pdb=" N VAL B 222 " pdb=" C VAL B 222 " pdb=" CB VAL B 222 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA LEU A 70 " pdb=" N LEU A 70 " pdb=" C LEU A 70 " pdb=" CB LEU A 70 " 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 VAL A 195 " pdb=" N VAL A 195 " pdb=" C VAL A 195 " pdb=" CB VAL A 195 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 824 not shown) Planarity restraints: 964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 25 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 26 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 340 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 341 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 28 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO C 29 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 29 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 29 " 0.016 5.00e-02 4.00e+02 ... (remaining 961 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1376 2.80 - 3.33: 5197 3.33 - 3.85: 8567 3.85 - 4.38: 9625 4.38 - 4.90: 16927 Nonbonded interactions: 41692 Sorted by model distance: nonbonded pdb=" OE2 GLU A 203 " pdb=" NH2 ARG A 323 " model vdw 2.278 3.120 nonbonded pdb=" O LYS B 70 " pdb=" N PHE B 72 " model vdw 2.283 3.120 nonbonded pdb=" O THR B 252 " pdb=" OG SER B 255 " model vdw 2.284 3.040 nonbonded pdb=" O ILE A 59 " pdb=" NZ LYS B 96 " model vdw 2.300 3.120 nonbonded pdb=" NE2 GLN C 27 " pdb=" O HIS A 143 " model vdw 2.332 3.120 ... (remaining 41687 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.002 0.031 5644 Z= 0.145 Angle : 0.551 7.630 7625 Z= 0.276 Chirality : 0.041 0.141 827 Planarity : 0.004 0.041 964 Dihedral : 14.159 80.877 2124 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.33), residues: 655 helix: 1.66 (0.31), residues: 311 sheet: 1.88 (1.30), residues: 13 loop : -0.75 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 38 HIS 0.001 0.000 HIS A 34 PHE 0.011 0.001 PHE B 140 TYR 0.007 0.001 TYR C 25 ARG 0.008 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.706 Fit side-chains REVERT: D 1617 MET cc_start: 0.5644 (mmp) cc_final: 0.4255 (tmm) REVERT: A 61 MET cc_start: 0.7989 (mmm) cc_final: 0.7777 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1666 time to fit residues: 21.2101 Evaluate side-chains 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091121 restraints weight = 31673.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095732 restraints weight = 15809.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096364 restraints weight = 9441.979| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5644 Z= 0.262 Angle : 0.592 10.857 7625 Z= 0.296 Chirality : 0.044 0.150 827 Planarity : 0.004 0.033 964 Dihedral : 3.827 17.339 728 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.83 % Allowed : 7.97 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.32), residues: 655 helix: 1.42 (0.30), residues: 317 sheet: -0.41 (0.94), residues: 25 loop : -0.48 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 38 HIS 0.005 0.001 HIS A 310 PHE 0.010 0.001 PHE A 180 TYR 0.014 0.001 TYR B 184 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.690 Fit side-chains REVERT: D 1617 MET cc_start: 0.6038 (mmp) cc_final: 0.4412 (tmm) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.1346 time to fit residues: 13.7140 Evaluate side-chains 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN D1631 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.090967 restraints weight = 26493.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096047 restraints weight = 12431.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098629 restraints weight = 5814.739| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5644 Z= 0.174 Angle : 0.532 8.308 7625 Z= 0.263 Chirality : 0.042 0.139 827 Planarity : 0.004 0.032 964 Dihedral : 3.743 15.642 728 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.16 % Allowed : 10.13 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.33), residues: 655 helix: 1.48 (0.30), residues: 319 sheet: -0.17 (0.95), residues: 25 loop : -0.39 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 38 HIS 0.005 0.001 HIS D1631 PHE 0.010 0.001 PHE B 44 TYR 0.008 0.001 TYR B 184 ARG 0.007 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.585 Fit side-chains REVERT: D 1617 MET cc_start: 0.5947 (mmp) cc_final: 0.4454 (tmm) REVERT: A 107 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9128 (mm) REVERT: B 138 CYS cc_start: 0.8986 (t) cc_final: 0.8771 (t) outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 0.1279 time to fit residues: 13.8372 Evaluate side-chains 70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088510 restraints weight = 20365.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091723 restraints weight = 10886.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093789 restraints weight = 6689.617| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5644 Z= 0.271 Angle : 0.565 6.294 7625 Z= 0.285 Chirality : 0.044 0.162 827 Planarity : 0.004 0.046 964 Dihedral : 3.966 15.226 728 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.33 % Allowed : 11.30 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.33), residues: 655 helix: 1.17 (0.29), residues: 320 sheet: -0.16 (0.94), residues: 25 loop : -0.42 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 38 HIS 0.003 0.001 HIS A 88 PHE 0.010 0.001 PHE A 180 TYR 0.013 0.001 TYR B 184 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.530 Fit side-chains REVERT: D 1617 MET cc_start: 0.6233 (mmp) cc_final: 0.4389 (ppp) REVERT: B 38 TRP cc_start: 0.8330 (t60) cc_final: 0.7898 (t60) REVERT: B 132 MET cc_start: 0.7695 (tpt) cc_final: 0.7324 (tpp) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1365 time to fit residues: 13.8204 Evaluate side-chains 66 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 40 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.089907 restraints weight = 28241.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094665 restraints weight = 12895.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097226 restraints weight = 6952.084| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5644 Z= 0.170 Angle : 0.527 8.892 7625 Z= 0.261 Chirality : 0.042 0.159 827 Planarity : 0.004 0.043 964 Dihedral : 3.834 15.001 728 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.16 % Allowed : 12.46 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.33), residues: 655 helix: 1.35 (0.29), residues: 320 sheet: -0.02 (0.97), residues: 25 loop : -0.32 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 38 HIS 0.004 0.001 HIS D1631 PHE 0.010 0.001 PHE B 44 TYR 0.008 0.001 TYR B 76 ARG 0.001 0.000 ARG D1619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.633 Fit side-chains REVERT: D 1617 MET cc_start: 0.6199 (mmp) cc_final: 0.4486 (ppp) REVERT: A 107 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9147 (mm) REVERT: B 246 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7354 (mm-30) outliers start: 13 outliers final: 6 residues processed: 79 average time/residue: 0.1290 time to fit residues: 14.7514 Evaluate side-chains 70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.0010 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090309 restraints weight = 32916.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095273 restraints weight = 15538.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096045 restraints weight = 8710.620| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5644 Z= 0.193 Angle : 0.551 7.851 7625 Z= 0.271 Chirality : 0.042 0.161 827 Planarity : 0.004 0.042 964 Dihedral : 3.833 14.749 728 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.99 % Allowed : 13.79 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.33), residues: 655 helix: 1.30 (0.29), residues: 320 sheet: -0.01 (0.98), residues: 25 loop : -0.31 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 38 HIS 0.005 0.001 HIS D1631 PHE 0.010 0.001 PHE B 44 TYR 0.009 0.001 TYR B 76 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.705 Fit side-chains REVERT: D 1617 MET cc_start: 0.6311 (mmp) cc_final: 0.4550 (ppp) REVERT: A 107 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9115 (mm) REVERT: B 132 MET cc_start: 0.7660 (tpt) cc_final: 0.7289 (tpp) REVERT: B 246 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6786 (mm-30) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.1342 time to fit residues: 15.0174 Evaluate side-chains 74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088976 restraints weight = 27617.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093970 restraints weight = 12914.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096805 restraints weight = 5954.978| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5644 Z= 0.197 Angle : 0.544 9.281 7625 Z= 0.268 Chirality : 0.042 0.161 827 Planarity : 0.004 0.041 964 Dihedral : 3.851 16.326 728 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.49 % Allowed : 14.29 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.33), residues: 655 helix: 1.33 (0.29), residues: 320 sheet: -0.02 (1.00), residues: 25 loop : -0.31 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 38 HIS 0.004 0.001 HIS D1631 PHE 0.009 0.001 PHE B 44 TYR 0.009 0.001 TYR B 76 ARG 0.001 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.679 Fit side-chains REVERT: D 1617 MET cc_start: 0.6143 (mmp) cc_final: 0.4526 (ppp) REVERT: A 107 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9158 (mm) REVERT: B 132 MET cc_start: 0.7647 (tpt) cc_final: 0.7272 (tpp) REVERT: B 246 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6779 (mm-30) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.1254 time to fit residues: 13.9663 Evaluate side-chains 75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 171 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089918 restraints weight = 31348.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094740 restraints weight = 14244.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096329 restraints weight = 7675.357| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5644 Z= 0.177 Angle : 0.550 9.691 7625 Z= 0.271 Chirality : 0.042 0.157 827 Planarity : 0.004 0.041 964 Dihedral : 3.820 17.360 728 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.16 % Allowed : 15.12 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.33), residues: 655 helix: 1.37 (0.29), residues: 320 sheet: 0.00 (1.02), residues: 25 loop : -0.27 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 38 HIS 0.005 0.001 HIS D1631 PHE 0.029 0.001 PHE A 261 TYR 0.008 0.001 TYR B 76 ARG 0.002 0.000 ARG D1619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.678 Fit side-chains REVERT: D 1617 MET cc_start: 0.6273 (mmp) cc_final: 0.4572 (ppp) REVERT: A 107 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9132 (mm) REVERT: B 132 MET cc_start: 0.7648 (tpt) cc_final: 0.7274 (tpp) REVERT: B 137 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 141 TYR cc_start: 0.8119 (m-10) cc_final: 0.7769 (m-10) REVERT: B 220 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7589 (pp) REVERT: B 246 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6518 (mm-30) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.1366 time to fit residues: 15.2588 Evaluate side-chains 75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089911 restraints weight = 27841.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095287 restraints weight = 13247.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096701 restraints weight = 6869.280| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5644 Z= 0.193 Angle : 0.555 9.308 7625 Z= 0.274 Chirality : 0.042 0.166 827 Planarity : 0.004 0.042 964 Dihedral : 3.892 21.306 728 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.66 % Allowed : 15.12 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.33), residues: 655 helix: 1.32 (0.29), residues: 320 sheet: -0.00 (1.03), residues: 25 loop : -0.29 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 38 HIS 0.005 0.001 HIS D1631 PHE 0.027 0.001 PHE A 261 TYR 0.009 0.001 TYR B 76 ARG 0.001 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.685 Fit side-chains REVERT: D 1617 MET cc_start: 0.6176 (mmp) cc_final: 0.4510 (ppp) REVERT: A 107 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9152 (mm) REVERT: B 132 MET cc_start: 0.7672 (tpt) cc_final: 0.7316 (tpp) REVERT: B 139 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8746 (tt0) REVERT: B 220 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7589 (pp) outliers start: 15 outliers final: 8 residues processed: 78 average time/residue: 0.1382 time to fit residues: 15.2863 Evaluate side-chains 75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.0570 chunk 33 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.110751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090321 restraints weight = 17824.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093544 restraints weight = 9076.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095795 restraints weight = 5780.617| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5644 Z= 0.182 Angle : 0.557 10.084 7625 Z= 0.276 Chirality : 0.042 0.164 827 Planarity : 0.004 0.042 964 Dihedral : 3.911 22.243 728 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.99 % Allowed : 16.11 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.33), residues: 655 helix: 1.28 (0.29), residues: 320 sheet: 0.04 (1.02), residues: 25 loop : -0.28 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 38 HIS 0.005 0.001 HIS D1631 PHE 0.026 0.001 PHE A 261 TYR 0.008 0.001 TYR B 76 ARG 0.001 0.000 ARG C 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.622 Fit side-chains REVERT: D 1617 MET cc_start: 0.6067 (mmp) cc_final: 0.4518 (ppp) REVERT: A 107 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9181 (mm) REVERT: B 132 MET cc_start: 0.7610 (tpt) cc_final: 0.7288 (tpp) REVERT: B 137 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6789 (tm-30) REVERT: B 139 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8646 (tt0) REVERT: B 141 TYR cc_start: 0.7882 (m-10) cc_final: 0.7540 (m-10) REVERT: B 220 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7541 (pp) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.1250 time to fit residues: 13.6572 Evaluate side-chains 75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090998 restraints weight = 25723.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096160 restraints weight = 11950.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099115 restraints weight = 5674.235| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5644 Z= 0.155 Angle : 0.534 9.969 7625 Z= 0.265 Chirality : 0.041 0.133 827 Planarity : 0.004 0.043 964 Dihedral : 3.735 17.179 728 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.99 % Allowed : 16.11 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.33), residues: 655 helix: 1.39 (0.29), residues: 320 sheet: 0.01 (0.97), residues: 25 loop : -0.24 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 38 HIS 0.006 0.001 HIS D1631 PHE 0.026 0.001 PHE A 261 TYR 0.007 0.001 TYR B 76 ARG 0.001 0.000 ARG D1619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.33 seconds wall clock time: 33 minutes 51.31 seconds (2031.31 seconds total)