Starting phenix.real_space_refine (version: dev) on Fri Feb 17 13:09:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/02_2023/7y4s_33606.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/02_2023/7y4s_33606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/02_2023/7y4s_33606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/02_2023/7y4s_33606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/02_2023/7y4s_33606.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/02_2023/7y4s_33606.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.097 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4940 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2470 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2470 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 149 Time building chain proxies: 3.19, per 1000 atoms: 0.65 Number of scatterers: 4940 At special positions: 0 Unit cell: (103.455, 176.605, 83.6, 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 12 16.00 O 890 8.00 N 912 7.00 C 3126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.96 Conformation dependent library (CDL) restraints added in 794.5 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1288 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 40.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 125 through 228 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 235 through 254 removed outlier: 4.212A pdb=" N CYS A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.749A pdb=" N PHE A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 228 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 235 through 254 removed outlier: 4.212A pdb=" N CYS B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.749A pdb=" N PHE B 281 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 304 removed outlier: 3.556A pdb=" N VAL A 311 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 467 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 424 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 440 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A 426 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AA4, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.556A pdb=" N VAL B 311 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 467 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 424 " --> pdb=" O ALA B 440 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 440 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE B 426 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AA6, first strand: chain 'B' and resid 385 through 386 299 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1722 1.34 - 1.46: 918 1.46 - 1.58: 2394 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 5052 Sorted by residual: bond pdb=" CB VAL A 375 " pdb=" CG1 VAL A 375 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.99e+00 bond pdb=" CB VAL B 375 " pdb=" CG1 VAL B 375 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CB VAL A 375 " pdb=" CG2 VAL A 375 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" CB VAL B 375 " pdb=" CG2 VAL B 375 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" CA PRO B 448 " pdb=" C PRO B 448 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 5047 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.52: 160 105.52 - 112.65: 2610 112.65 - 119.78: 1591 119.78 - 126.91: 2451 126.91 - 134.04: 82 Bond angle restraints: 6894 Sorted by residual: angle pdb=" C VAL B 375 " pdb=" CA VAL B 375 " pdb=" CB VAL B 375 " ideal model delta sigma weight residual 109.33 112.78 -3.45 9.80e-01 1.04e+00 1.24e+01 angle pdb=" C ASP B 459 " pdb=" N LYS B 460 " pdb=" CA LYS B 460 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C ASP A 459 " pdb=" N LYS A 460 " pdb=" CA LYS A 460 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA VAL B 375 " pdb=" C VAL B 375 " pdb=" N PRO B 376 " ideal model delta sigma weight residual 116.57 119.49 -2.92 9.80e-01 1.04e+00 8.90e+00 angle pdb=" CA ARG A 404 " pdb=" CB ARG A 404 " pdb=" CG ARG A 404 " ideal model delta sigma weight residual 114.10 119.40 -5.30 2.00e+00 2.50e-01 7.02e+00 ... (remaining 6889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 2762 15.14 - 30.28: 216 30.28 - 45.41: 50 45.41 - 60.55: 8 60.55 - 75.69: 8 Dihedral angle restraints: 3044 sinusoidal: 1066 harmonic: 1978 Sorted by residual: dihedral pdb=" CA SER A 430 " pdb=" C SER A 430 " pdb=" N ASP A 431 " pdb=" CA ASP A 431 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA SER B 430 " pdb=" C SER B 430 " pdb=" N ASP B 431 " pdb=" CA ASP B 431 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB MET A 285 " pdb=" CG MET A 285 " pdb=" SD MET A 285 " pdb=" CE MET A 285 " ideal model delta sinusoidal sigma weight residual 60.00 119.60 -59.60 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 470 0.031 - 0.061: 203 0.061 - 0.092: 70 0.092 - 0.122: 19 0.122 - 0.153: 12 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA VAL B 395 " pdb=" N VAL B 395 " pdb=" C VAL B 395 " pdb=" CB VAL B 395 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA VAL A 395 " pdb=" N VAL A 395 " pdb=" C VAL A 395 " pdb=" CB VAL A 395 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL B 304 " pdb=" N VAL B 304 " pdb=" C VAL B 304 " pdb=" CB VAL B 304 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 771 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 399 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 400 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 399 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 400 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 400 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 400 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 375 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO A 376 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.030 5.00e-02 4.00e+02 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1698 2.88 - 3.38: 4794 3.38 - 3.89: 7875 3.89 - 4.39: 8095 4.39 - 4.90: 14623 Nonbonded interactions: 37085 Sorted by model distance: nonbonded pdb=" OE1 GLU B 348 " pdb=" NH1 ARG B 412 " model vdw 2.373 2.520 nonbonded pdb=" OE1 GLU A 348 " pdb=" NH1 ARG A 412 " model vdw 2.373 2.520 nonbonded pdb=" O THR A 292 " pdb=" N HIS A 337 " model vdw 2.407 2.520 nonbonded pdb=" O THR B 292 " pdb=" N HIS B 337 " model vdw 2.407 2.520 nonbonded pdb=" OH TYR A 346 " pdb=" OE2 GLU A 348 " model vdw 2.513 2.440 ... (remaining 37080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3126 2.51 5 N 912 2.21 5 O 890 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.000 Extract box with map and model: 4.120 Check model and map are aligned: 0.080 Process input model: 17.070 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 5052 Z= 0.276 Angle : 0.740 8.109 6894 Z= 0.383 Chirality : 0.042 0.153 774 Planarity : 0.008 0.064 928 Dihedral : 12.744 75.690 1756 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.31), residues: 678 helix: 3.05 (0.26), residues: 276 sheet: -0.87 (0.46), residues: 120 loop : -0.26 (0.35), residues: 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.627 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.2561 time to fit residues: 32.5492 Evaluate side-chains 72 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0748 time to fit residues: 0.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5052 Z= 0.200 Angle : 0.552 5.260 6894 Z= 0.274 Chirality : 0.038 0.122 774 Planarity : 0.006 0.057 928 Dihedral : 3.939 14.544 738 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.33), residues: 678 helix: 4.24 (0.29), residues: 246 sheet: -0.85 (0.46), residues: 122 loop : 0.09 (0.33), residues: 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.571 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 91 average time/residue: 0.2760 time to fit residues: 30.1047 Evaluate side-chains 68 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0548 time to fit residues: 1.2522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 50.0000 chunk 19 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 0.0020 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 338 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 338 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5052 Z= 0.197 Angle : 0.553 8.504 6894 Z= 0.270 Chirality : 0.038 0.119 774 Planarity : 0.005 0.051 928 Dihedral : 3.819 14.346 738 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.33), residues: 678 helix: 4.42 (0.30), residues: 246 sheet: -0.87 (0.47), residues: 122 loop : 0.18 (0.34), residues: 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.598 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2494 time to fit residues: 21.5275 Evaluate side-chains 67 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0490 time to fit residues: 1.1596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 5052 Z= 0.383 Angle : 0.612 5.914 6894 Z= 0.298 Chirality : 0.040 0.122 774 Planarity : 0.006 0.049 928 Dihedral : 4.127 16.028 738 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.34), residues: 678 helix: 4.42 (0.30), residues: 246 sheet: -1.52 (0.46), residues: 122 loop : 0.55 (0.35), residues: 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.621 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 0.2392 time to fit residues: 22.3758 Evaluate side-chains 68 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0865 time to fit residues: 1.8421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN B 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5052 Z= 0.270 Angle : 0.572 6.030 6894 Z= 0.280 Chirality : 0.039 0.127 774 Planarity : 0.005 0.049 928 Dihedral : 3.975 15.530 738 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.34), residues: 678 helix: 4.50 (0.29), residues: 246 sheet: -1.57 (0.46), residues: 122 loop : 0.66 (0.35), residues: 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.581 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.2562 time to fit residues: 21.3678 Evaluate side-chains 60 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0467 time to fit residues: 0.9436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 0.0050 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 50.0000 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5052 Z= 0.222 Angle : 0.548 5.463 6894 Z= 0.269 Chirality : 0.038 0.133 774 Planarity : 0.005 0.048 928 Dihedral : 3.880 15.347 738 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.34), residues: 678 helix: 4.54 (0.29), residues: 246 sheet: -1.45 (0.45), residues: 128 loop : 0.66 (0.36), residues: 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.587 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.2510 time to fit residues: 20.6024 Evaluate side-chains 64 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0487 time to fit residues: 1.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5052 Z= 0.219 Angle : 0.539 5.413 6894 Z= 0.266 Chirality : 0.038 0.137 774 Planarity : 0.005 0.048 928 Dihedral : 3.849 15.185 738 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.34), residues: 678 helix: 4.60 (0.29), residues: 246 sheet: -1.44 (0.44), residues: 128 loop : 0.70 (0.36), residues: 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.601 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 63 average time/residue: 0.2764 time to fit residues: 21.2362 Evaluate side-chains 59 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0467 time to fit residues: 0.8832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 59 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 264 GLN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5052 Z= 0.212 Angle : 0.542 5.667 6894 Z= 0.268 Chirality : 0.038 0.140 774 Planarity : 0.005 0.048 928 Dihedral : 3.792 15.138 738 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.34), residues: 678 helix: 4.58 (0.29), residues: 246 sheet: -1.51 (0.46), residues: 122 loop : 0.74 (0.36), residues: 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.593 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.2836 time to fit residues: 21.9199 Evaluate side-chains 60 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0599 time to fit residues: 1.0389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.0030 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.0030 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.0070 chunk 44 optimal weight: 10.0000 overall best weight: 0.2218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 264 GLN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 5052 Z= 0.152 Angle : 0.523 6.136 6894 Z= 0.259 Chirality : 0.038 0.130 774 Planarity : 0.005 0.049 928 Dihedral : 3.681 15.050 738 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.34), residues: 678 helix: 4.59 (0.28), residues: 246 sheet: -1.29 (0.45), residues: 128 loop : 0.71 (0.36), residues: 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.608 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.2770 time to fit residues: 21.2261 Evaluate side-chains 57 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0497 time to fit residues: 0.8175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN B 338 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 5052 Z= 0.277 Angle : 0.567 6.164 6894 Z= 0.279 Chirality : 0.039 0.137 774 Planarity : 0.005 0.048 928 Dihedral : 3.806 15.286 738 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.34), residues: 678 helix: 4.62 (0.29), residues: 246 sheet: -1.50 (0.46), residues: 122 loop : 0.77 (0.36), residues: 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.635 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 0.2770 time to fit residues: 21.3987 Evaluate side-chains 62 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0814 time to fit residues: 0.8489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 338 GLN A 339 GLN B 264 GLN B 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145581 restraints weight = 5757.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141356 restraints weight = 7729.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143739 restraints weight = 8283.099| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5052 Z= 0.214 Angle : 0.540 6.159 6894 Z= 0.265 Chirality : 0.038 0.133 774 Planarity : 0.005 0.048 928 Dihedral : 3.767 15.496 738 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.34), residues: 678 helix: 4.63 (0.28), residues: 246 sheet: -1.48 (0.46), residues: 122 loop : 0.82 (0.36), residues: 310 =============================================================================== Job complete usr+sys time: 1363.54 seconds wall clock time: 25 minutes 25.36 seconds (1525.36 seconds total)