Starting phenix.real_space_refine on Mon Sep 23 18:09:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/09_2024/8dki_27489_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/09_2024/8dki_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/09_2024/8dki_27489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/09_2024/8dki_27489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/09_2024/8dki_27489_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/09_2024/8dki_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-5461/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: 3.77, per 1000 atoms: 0.86 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: 1.12 Conformation dependent library (CDL) restraints added in 465.7 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: 0.50 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: 1.30 Time building geometry restraints manager: 1.32 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: 1.910 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.920 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.417 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: 0.1708 time to fit residues: 21.7880 Evaluate side-chains 84 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.554 Fit side-chains REVERT: P 140 ILE cc_start: 0.8687 (tt) cc_final: 0.8484 (tt) REVERT: P 356 LEU cc_start: 0.8642 (mp) cc_final: 0.8395 (mp) REVERT: A 31 ASN cc_start: 0.8475 (m-40) cc_final: 0.8267 (m-40) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1495 time to fit residues: 18.0867 Evaluate side-chains 85 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1365 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= 0.186 Angle : 0.568 7.221 6117 Z= 0.290 Chirality : 0.042 0.140 692 Planarity : 0.004 0.044 765 Dihedral : 4.474 22.457 595 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.48 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: -0.20 (0.38), residues: 546 helix: 1.83 (0.38), residues: 200 sheet: -1.06 (0.44), residues: 150 loop : -1.38 (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 289 TYR 0.016 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 fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.467 Fit side-chains REVERT: P 82 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9212 (m) REVERT: P 140 ILE cc_start: 0.8675 (tt) cc_final: 0.8469 (tt) REVERT: P 356 LEU cc_start: 0.8543 (mp) cc_final: 0.8273 (mp) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.1467 time to fit residues: 19.1417 Evaluate side-chains 91 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1552 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= 0.220 Angle : 0.580 6.956 6117 Z= 0.296 Chirality : 0.043 0.143 692 Planarity : 0.004 0.042 765 Dihedral : 4.474 22.467 595 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.70 % Allowed : 13.90 % Favored : 83.40 % 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: 1.86 (0.38), residues: 200 sheet: -1.03 (0.44), residues: 150 loop : -1.37 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.015 0.001 PHE A 69 TYR 0.016 0.002 TYR P 185 ARG 0.003 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 99 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.500 Fit side-chains REVERT: P 82 VAL cc_start: 0.9448 (OUTLIER) cc_final: 0.9218 (m) REVERT: P 356 LEU cc_start: 0.8589 (mp) cc_final: 0.8313 (mp) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1407 time to fit residues: 16.9911 Evaluate side-chains 90 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 127 ASN A 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4485 Z= 0.384 Angle : 0.643 7.446 6117 Z= 0.329 Chirality : 0.046 0.152 692 Planarity : 0.004 0.042 765 Dihedral : 4.774 23.351 595 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.53 % Allowed : 15.15 % Favored : 81.33 % 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: -0.37 (0.37), residues: 546 helix: 1.72 (0.37), residues: 200 sheet: -1.16 (0.44), residues: 152 loop : -1.51 (0.44), residues: 194 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 0.019 0.002 PHE A 69 TYR 0.017 0.002 TYR P 134 ARG 0.004 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 fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.499 Fit side-chains REVERT: P 356 LEU cc_start: 0.8698 (mp) cc_final: 0.8422 (mp) REVERT: B 61 ARG cc_start: 0.8333 (ttm170) cc_final: 0.8044 (ttm170) outliers start: 17 outliers final: 15 residues processed: 93 average time/residue: 0.1460 time to fit residues: 17.7110 Evaluate side-chains 94 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 A residue 52 SER 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 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4485 Z= 0.203 Angle : 0.572 7.103 6117 Z= 0.292 Chirality : 0.043 0.141 692 Planarity : 0.004 0.041 765 Dihedral : 4.521 22.453 595 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.70 % Allowed : 16.80 % Favored : 80.50 % 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: 1.85 (0.38), residues: 200 sheet: -1.04 (0.44), residues: 151 loop : -1.39 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 PHE 0.016 0.001 PHE P 176 TYR 0.017 0.001 TYR P 185 ARG 0.004 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 98 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.481 Fit side-chains REVERT: P 356 LEU cc_start: 0.8659 (mp) cc_final: 0.8391 (mp) REVERT: A 55 GLU cc_start: 0.7105 (mp0) cc_final: 0.6902 (mp0) outliers start: 13 outliers final: 12 residues processed: 93 average time/residue: 0.1503 time to fit residues: 17.9143 Evaluate side-chains 93 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 GLN A 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4485 Z= 0.363 Angle : 0.632 7.400 6117 Z= 0.323 Chirality : 0.046 0.149 692 Planarity : 0.004 0.040 765 Dihedral : 4.767 23.440 595 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.32 % Allowed : 17.01 % Favored : 79.67 % 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: 1.54 (0.37), residues: 206 sheet: -1.15 (0.44), residues: 151 loop : -1.57 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.022 0.002 PHE A 69 TYR 0.019 0.002 TYR P 185 ARG 0.006 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 100 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.435 Fit side-chains REVERT: P 148 MET cc_start: 0.8309 (ttp) cc_final: 0.7710 (ttp) REVERT: P 174 SER cc_start: 0.8399 (p) cc_final: 0.8138 (p) REVERT: P 356 LEU cc_start: 0.8721 (mp) cc_final: 0.8412 (mp) REVERT: B 61 ARG cc_start: 0.8343 (ttm170) cc_final: 0.8079 (ttm170) outliers start: 16 outliers final: 14 residues processed: 95 average time/residue: 0.1417 time to fit residues: 17.6222 Evaluate side-chains 96 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4485 Z= 0.243 Angle : 0.592 7.705 6117 Z= 0.302 Chirality : 0.044 0.145 692 Planarity : 0.004 0.040 765 Dihedral : 4.596 22.931 595 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.11 % Allowed : 17.43 % Favored : 79.46 % 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: -0.35 (0.38), residues: 546 helix: 1.58 (0.37), residues: 206 sheet: -1.11 (0.44), residues: 151 loop : -1.44 (0.45), residues: 189 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 0.017 0.001 PHE A 69 TYR 0.013 0.001 TYR P 134 ARG 0.006 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 101 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.478 Fit side-chains REVERT: P 148 MET cc_start: 0.8208 (ttp) cc_final: 0.7616 (ttp) REVERT: P 174 SER cc_start: 0.8422 (p) cc_final: 0.8165 (p) REVERT: P 180 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7719 (mt) outliers start: 15 outliers final: 13 residues processed: 95 average time/residue: 0.1520 time to fit residues: 19.2811 Evaluate side-chains 97 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 180 LEU 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 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4485 Z= 0.247 Angle : 0.601 7.939 6117 Z= 0.305 Chirality : 0.044 0.145 692 Planarity : 0.004 0.039 765 Dihedral : 4.585 22.926 595 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.11 % Allowed : 17.63 % Favored : 79.25 % 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: -0.36 (0.38), residues: 546 helix: 1.59 (0.37), residues: 206 sheet: -1.11 (0.44), residues: 150 loop : -1.47 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 182 HIS 0.001 0.001 HIS P 211 PHE 0.027 0.002 PHE A 69 TYR 0.014 0.001 TYR P 134 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 101 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.481 Fit side-chains REVERT: P 174 SER cc_start: 0.8397 (p) cc_final: 0.8165 (p) REVERT: P 356 LEU cc_start: 0.8687 (mp) cc_final: 0.8380 (mp) outliers start: 15 outliers final: 14 residues processed: 96 average time/residue: 0.1410 time to fit residues: 17.5626 Evaluate side-chains 96 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1979 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= 0.226 Angle : 0.598 8.069 6117 Z= 0.303 Chirality : 0.044 0.144 692 Planarity : 0.004 0.039 765 Dihedral : 4.519 22.696 595 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.90 % Allowed : 17.63 % Favored : 79.46 % 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: -0.24 (0.38), residues: 546 helix: 1.80 (0.38), residues: 200 sheet: -1.11 (0.44), residues: 151 loop : -1.37 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 182 HIS 0.001 0.001 HIS P 211 PHE 0.022 0.002 PHE P 207 TYR 0.013 0.001 TYR P 134 ARG 0.007 0.000 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 98 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.476 Fit side-chains REVERT: P 174 SER cc_start: 0.8414 (p) cc_final: 0.8174 (p) REVERT: P 185 TYR cc_start: 0.7842 (t80) cc_final: 0.7634 (t80) REVERT: P 356 LEU cc_start: 0.8668 (mp) cc_final: 0.8376 (mp) outliers start: 14 outliers final: 13 residues processed: 93 average time/residue: 0.1460 time to fit residues: 17.6969 Evaluate side-chains 95 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 96 GLN P 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112189 restraints weight = 5418.872| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.41 r_work: 0.3099 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4485 Z= 0.380 Angle : 0.662 7.920 6117 Z= 0.335 Chirality : 0.047 0.150 692 Planarity : 0.005 0.039 765 Dihedral : 4.793 23.513 595 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.90 % Allowed : 17.63 % Favored : 79.46 % 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: -0.52 (0.37), residues: 546 helix: 1.47 (0.37), residues: 206 sheet: -1.14 (0.44), residues: 150 loop : -1.63 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.027 0.002 PHE A 69 TYR 0.017 0.002 TYR P 134 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: 1393.48 seconds wall clock time: 25 minutes 24.15 seconds (1524.15 seconds total)