Starting phenix.real_space_refine on Thu Mar 6 01:36:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dki_27489/03_2025/8dki_27489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dki_27489/03_2025/8dki_27489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dki_27489/03_2025/8dki_27489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dki_27489/03_2025/8dki_27489.map" model { file = "/net/cci-nas-00/data/ceres_data/8dki_27489/03_2025/8dki_27489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dki_27489/03_2025/8dki_27489_neut.cif" } resolution = 3.32 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= 0.004 sd= 0.070 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 15 5.16 5 C 2858 2.51 5 N 703 2.21 5 O 789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4365 Number of models: 1 Model: "" Number of chains: 3 Chain: "P" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2679 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 871 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 3.39, per 1000 atoms: 0.78 Number of scatterers: 4365 At special positions: 0 Unit cell: (78.492, 64.988, 114.784, 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 15 16.00 O 789 8.00 N 703 7.00 C 2858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 509.9 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 7 sheets defined 38.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'P' and resid 120 through 141 Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.618A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 180 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 Processing helix chain 'P' and resid 234 through 257 removed outlier: 3.662A pdb=" N VAL P 257 " --> pdb=" O ILE P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 279 removed outlier: 3.586A pdb=" N PHE P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE P 269 " --> pdb=" O PHE P 265 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 292 removed outlier: 3.748A pdb=" N TYR P 291 " --> pdb=" O MET P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.685A pdb=" N VAL P 302 " --> pdb=" O SER P 298 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR P 321 " --> pdb=" O PHE P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 330 Processing helix chain 'P' and resid 332 through 355 removed outlier: 3.627A pdb=" N PHE P 336 " --> pdb=" O ASP P 332 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.002A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.762A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 26 through 27 removed outlier: 3.831A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 31 through 35 removed outlier: 3.934A pdb=" N VAL P 32 " --> pdb=" O ARG P 114 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.582A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.648A pdb=" N ILE B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.426A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.351A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 639 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: 1.06 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 885 1.33 - 1.45: 1158 1.45 - 1.57: 2420 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4485 Sorted by residual: bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.19e+01 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.51e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.34e-02 5.57e+03 6.21e+00 bond pdb=" C PHE P 317 " pdb=" O PHE P 317 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.19e-02 7.06e+03 5.45e+00 bond pdb=" C MET P 316 " pdb=" O MET P 316 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.26e-02 6.30e+03 4.55e+00 ... (remaining 4480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 5902 1.50 - 2.99: 161 2.99 - 4.49: 44 4.49 - 5.99: 8 5.99 - 7.48: 2 Bond angle restraints: 6117 Sorted by residual: angle pdb=" C PRO A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N MET P 316 " pdb=" CA MET P 316 " pdb=" C MET P 316 " ideal model delta sigma weight residual 111.82 108.02 3.80 1.16e+00 7.43e-01 1.08e+01 angle pdb=" CA THR P 261 " pdb=" C THR P 261 " pdb=" O THR P 261 " ideal model delta sigma weight residual 121.87 118.14 3.73 1.16e+00 7.43e-01 1.03e+01 angle pdb=" N ILE P 69 " pdb=" CA ILE P 69 " pdb=" C ILE P 69 " ideal model delta sigma weight residual 111.48 108.48 3.00 9.40e-01 1.13e+00 1.02e+01 angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 113.18 119.11 -5.93 2.37e+00 1.78e-01 6.27e+00 ... (remaining 6112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2333 17.95 - 35.90: 207 35.90 - 53.84: 30 53.84 - 71.79: 3 71.79 - 89.74: 5 Dihedral angle restraints: 2578 sinusoidal: 984 harmonic: 1594 Sorted by residual: dihedral pdb=" CA ARG P 47 " pdb=" C ARG P 47 " pdb=" N PRO P 48 " pdb=" CA PRO P 48 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG P 151 " pdb=" C ARG P 151 " pdb=" N ARG P 152 " pdb=" CA ARG P 152 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PRO A 41 " pdb=" C PRO A 41 " pdb=" N GLU A 42 " pdb=" CA GLU A 42 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 582 0.059 - 0.119: 97 0.119 - 0.178: 11 0.178 - 0.238: 1 0.238 - 0.297: 1 Chirality restraints: 692 Sorted by residual: chirality pdb=" CA LEU P 318 " pdb=" N LEU P 318 " pdb=" C LEU P 318 " pdb=" CB LEU P 318 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PHE P 317 " pdb=" N PHE P 317 " pdb=" C PHE P 317 " pdb=" CB PHE P 317 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL P 279 " pdb=" CA VAL P 279 " pdb=" CG1 VAL P 279 " pdb=" CG2 VAL P 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 689 not shown) Planarity restraints: 765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 182 " 0.015 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP P 182 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP P 182 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 182 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 182 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 182 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 182 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR P 143 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO P 144 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO P 144 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO P 144 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 341 " -0.014 2.00e-02 2.50e+03 1.27e-02 2.80e+00 pdb=" CG PHE P 341 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE P 341 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE P 341 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE P 341 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE P 341 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE P 341 " -0.001 2.00e-02 2.50e+03 ... (remaining 762 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 390 2.74 - 3.28: 4352 3.28 - 3.82: 7394 3.82 - 4.36: 8374 4.36 - 4.90: 14840 Nonbonded interactions: 35350 Sorted by model distance: nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR P 281 " pdb=" OD2 ASP P 305 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 7 " pdb=" OG SER A 21 " model vdw 2.256 3.040 nonbonded pdb=" NE2 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.292 3.120 nonbonded pdb=" O PRO P 49 " pdb=" OH TYR A 100 " model vdw 2.298 3.040 ... (remaining 35345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4485 Z= 0.225 Angle : 0.641 7.482 6117 Z= 0.347 Chirality : 0.046 0.297 692 Planarity : 0.004 0.047 765 Dihedral : 13.794 89.741 1554 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.21 % Allowed : 0.41 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.62 (0.37), residues: 546 helix: 1.17 (0.38), residues: 199 sheet: -1.09 (0.44), residues: 150 loop : -1.41 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.029 0.002 PHE P 341 TYR 0.012 0.001 TYR P 134 ARG 0.008 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.413 Fit side-chains REVERT: P 140 ILE cc_start: 0.8683 (tt) cc_final: 0.8455 (tt) REVERT: P 317 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6764 (t80) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1641 time to fit residues: 20.8815 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 317 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 96 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117610 restraints weight = 5202.855| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.06 r_work: 0.3163 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4485 Z= 0.348 Angle : 0.653 8.847 6117 Z= 0.331 Chirality : 0.045 0.154 692 Planarity : 0.005 0.048 765 Dihedral : 5.259 50.900 597 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.66 % Allowed : 9.54 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.38), residues: 546 helix: 1.61 (0.38), residues: 201 sheet: -1.17 (0.43), residues: 150 loop : -1.49 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.013 0.001 PHE P 240 TYR 0.020 0.002 TYR P 134 ARG 0.004 0.001 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.420 Fit side-chains REVERT: P 140 ILE cc_start: 0.8753 (tt) cc_final: 0.8543 (tt) REVERT: P 356 LEU cc_start: 0.8665 (mp) cc_final: 0.8372 (mp) REVERT: A 31 ASN cc_start: 0.8901 (m-40) cc_final: 0.8612 (m-40) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1433 time to fit residues: 17.1304 Evaluate side-chains 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 264 GLN A 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123736 restraints weight = 5122.198| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.12 r_work: 0.3219 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4485 Z= 0.189 Angle : 0.573 7.329 6117 Z= 0.293 Chirality : 0.042 0.141 692 Planarity : 0.004 0.044 765 Dihedral : 4.504 22.563 595 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.07 % Allowed : 12.45 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.22 (0.38), residues: 546 helix: 1.81 (0.38), residues: 200 sheet: -1.07 (0.44), residues: 150 loop : -1.39 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 PHE 0.011 0.001 PHE P 87 TYR 0.017 0.001 TYR P 134 ARG 0.003 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.490 Fit side-chains REVERT: P 140 ILE cc_start: 0.8731 (tt) cc_final: 0.8526 (tt) REVERT: P 356 LEU cc_start: 0.8580 (mp) cc_final: 0.8275 (mp) REVERT: A 31 ASN cc_start: 0.8888 (m-40) cc_final: 0.8603 (m-40) REVERT: A 55 GLU cc_start: 0.7799 (mp0) cc_final: 0.7523 (mp0) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.1490 time to fit residues: 19.3555 Evaluate side-chains 92 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.153298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118346 restraints weight = 5412.119| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.35 r_work: 0.3183 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4485 Z= 0.274 Angle : 0.600 7.334 6117 Z= 0.305 Chirality : 0.044 0.147 692 Planarity : 0.004 0.043 765 Dihedral : 4.569 22.884 595 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.11 % Allowed : 13.28 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.18 (0.38), residues: 546 helix: 1.80 (0.38), residues: 200 sheet: -0.89 (0.46), residues: 141 loop : -1.47 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.017 0.001 PHE A 69 TYR 0.016 0.002 TYR P 134 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.480 Fit side-chains REVERT: P 356 LEU cc_start: 0.8642 (mp) cc_final: 0.8333 (mp) REVERT: A 55 GLU cc_start: 0.7563 (mp0) cc_final: 0.7304 (mp0) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.1550 time to fit residues: 18.3010 Evaluate side-chains 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 127 ASN P 189 GLN A 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118923 restraints weight = 5516.484| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.40 r_work: 0.3215 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4485 Z= 0.240 Angle : 0.582 6.880 6117 Z= 0.298 Chirality : 0.043 0.144 692 Planarity : 0.004 0.042 765 Dihedral : 4.510 22.550 595 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.90 % Allowed : 15.35 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.16 (0.38), residues: 546 helix: 1.81 (0.38), residues: 200 sheet: -0.90 (0.46), residues: 142 loop : -1.42 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.014 0.001 PHE P 341 TYR 0.015 0.001 TYR P 185 ARG 0.002 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.441 Fit side-chains REVERT: P 148 MET cc_start: 0.8358 (ttp) cc_final: 0.7747 (ttp) REVERT: P 356 LEU cc_start: 0.8657 (mp) cc_final: 0.8384 (mp) REVERT: A 55 GLU cc_start: 0.7515 (mp0) cc_final: 0.7245 (mp0) outliers start: 14 outliers final: 14 residues processed: 93 average time/residue: 0.1457 time to fit residues: 17.5222 Evaluate side-chains 95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.150095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114888 restraints weight = 5447.475| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.36 r_work: 0.3140 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4485 Z= 0.399 Angle : 0.647 7.386 6117 Z= 0.330 Chirality : 0.046 0.151 692 Planarity : 0.004 0.042 765 Dihedral : 4.808 23.460 595 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.73 % Allowed : 16.39 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.45 (0.37), residues: 546 helix: 1.49 (0.37), residues: 206 sheet: -0.96 (0.46), residues: 142 loop : -1.68 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.022 0.002 PHE A 69 TYR 0.017 0.002 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.440 Fit side-chains REVERT: P 148 MET cc_start: 0.8355 (ttp) cc_final: 0.7718 (ttp) REVERT: P 356 LEU cc_start: 0.8720 (mp) cc_final: 0.8397 (mp) REVERT: A 55 GLU cc_start: 0.7727 (mp0) cc_final: 0.7427 (mp0) outliers start: 18 outliers final: 16 residues processed: 94 average time/residue: 0.1402 time to fit residues: 17.2190 Evaluate side-chains 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118373 restraints weight = 5471.145| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.38 r_work: 0.3182 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4485 Z= 0.236 Angle : 0.590 7.307 6117 Z= 0.303 Chirality : 0.044 0.144 692 Planarity : 0.004 0.041 765 Dihedral : 4.608 22.938 595 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.53 % Allowed : 17.43 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.38), residues: 546 helix: 1.58 (0.37), residues: 206 sheet: -0.93 (0.46), residues: 142 loop : -1.55 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 182 HIS 0.001 0.001 HIS P 211 PHE 0.015 0.001 PHE P 176 TYR 0.020 0.002 TYR P 185 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.448 Fit side-chains REVERT: A 55 GLU cc_start: 0.7490 (mp0) cc_final: 0.7219 (mp0) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.1357 time to fit residues: 17.5291 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118859 restraints weight = 5426.198| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.38 r_work: 0.3187 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4485 Z= 0.232 Angle : 0.587 7.768 6117 Z= 0.299 Chirality : 0.044 0.144 692 Planarity : 0.004 0.040 765 Dihedral : 4.541 22.736 595 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.11 % Allowed : 17.01 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.38), residues: 546 helix: 1.68 (0.38), residues: 206 sheet: -0.95 (0.46), residues: 142 loop : -1.50 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.026 0.001 PHE A 69 TYR 0.013 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.481 Fit side-chains REVERT: P 148 MET cc_start: 0.8261 (ttp) cc_final: 0.7876 (ttt) REVERT: P 356 LEU cc_start: 0.8683 (mp) cc_final: 0.8360 (mp) REVERT: A 55 GLU cc_start: 0.7497 (mp0) cc_final: 0.7206 (mp0) outliers start: 15 outliers final: 15 residues processed: 95 average time/residue: 0.1456 time to fit residues: 18.0709 Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 45 optimal weight: 0.0270 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 0.0270 chunk 4 optimal weight: 0.0040 overall best weight: 0.1108 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.161911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127082 restraints weight = 5463.259| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.46 r_work: 0.3296 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4485 Z= 0.145 Angle : 0.556 8.225 6117 Z= 0.283 Chirality : 0.042 0.136 692 Planarity : 0.004 0.039 765 Dihedral : 4.224 20.636 595 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.24 % Allowed : 18.88 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.08 (0.38), residues: 546 helix: 1.90 (0.37), residues: 200 sheet: -0.83 (0.47), residues: 139 loop : -1.41 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 132 HIS 0.001 0.000 HIS P 211 PHE 0.016 0.001 PHE P 289 TYR 0.012 0.001 TYR P 185 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.433 Fit side-chains REVERT: P 356 LEU cc_start: 0.8604 (mp) cc_final: 0.8319 (mp) REVERT: A 55 GLU cc_start: 0.7227 (mp0) cc_final: 0.6954 (mp0) outliers start: 6 outliers final: 6 residues processed: 105 average time/residue: 0.1533 time to fit residues: 20.4949 Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.0020 chunk 51 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.156567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123770 restraints weight = 5146.578| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.01 r_work: 0.3246 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4485 Z= 0.201 Angle : 0.592 7.972 6117 Z= 0.297 Chirality : 0.043 0.139 692 Planarity : 0.004 0.042 765 Dihedral : 4.297 21.591 595 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.24 % Allowed : 20.12 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.04 (0.39), residues: 546 helix: 2.01 (0.38), residues: 200 sheet: -0.81 (0.47), residues: 141 loop : -1.33 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 182 HIS 0.002 0.001 HIS P 211 PHE 0.019 0.001 PHE A 69 TYR 0.011 0.001 TYR P 226 ARG 0.010 0.001 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.453 Fit side-chains REVERT: P 174 SER cc_start: 0.8593 (p) cc_final: 0.8365 (p) REVERT: P 356 LEU cc_start: 0.8634 (mp) cc_final: 0.8322 (mp) REVERT: A 55 GLU cc_start: 0.7571 (mp0) cc_final: 0.7265 (mp0) outliers start: 6 outliers final: 6 residues processed: 98 average time/residue: 0.1666 time to fit residues: 20.7376 Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.3970 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.157452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124488 restraints weight = 5184.944| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.01 r_work: 0.3259 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4485 Z= 0.177 Angle : 0.584 8.695 6117 Z= 0.292 Chirality : 0.043 0.139 692 Planarity : 0.004 0.039 765 Dihedral : 4.270 21.387 595 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.45 % Allowed : 20.54 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.04 (0.39), residues: 546 helix: 2.01 (0.38), residues: 200 sheet: -0.87 (0.47), residues: 144 loop : -1.29 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 PHE 0.024 0.001 PHE P 207 TYR 0.010 0.001 TYR P 185 ARG 0.008 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.33 seconds wall clock time: 43 minutes 5.50 seconds (2585.50 seconds total)