Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:21:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/04_2023/7wr8_32718.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/04_2023/7wr8_32718.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/7wr8_32718/04_2023/7wr8_32718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/04_2023/7wr8_32718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/04_2023/7wr8_32718.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/04_2023/7wr8_32718.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= 0.026 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 2086 2.51 5 N 555 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 357": "NH1" <-> "NH2" Residue "R PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 442": "OD1" <-> "OD2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3286 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 780 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.44, per 1000 atoms: 0.74 Number of scatterers: 3286 At special positions: 0 Unit cell: (100.88, 62.4, 69.68, 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 630 8.00 N 555 7.00 C 2086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 454.9 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 9.6% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.925A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.319A pdb=" N VAL R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.912A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.804A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.668A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.631A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.353A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.522A pdb=" N SER A 17 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 83 " --> pdb=" O SER A 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.146A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.857A pdb=" N THR B 73 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.891A pdb=" N THR B 103 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 45 " --> pdb=" O GLN B 36 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 174 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: 0.81 Time building geometry restraints manager: 1.46 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: 813 1.33 - 1.45: 759 1.45 - 1.57: 1783 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3373 Sorted by residual: bond pdb=" CG LEU R 441 " pdb=" CD2 LEU R 441 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 bond pdb=" C GLU B 52 " pdb=" N ARG B 53 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.05e-02 9.07e+03 4.83e+00 bond pdb=" C ASP A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.72e+00 bond pdb=" C SER B 13 " pdb=" N PRO B 14 " ideal model delta sigma weight residual 1.332 1.357 -0.026 1.34e-02 5.57e+03 3.63e+00 bond pdb=" CB TRP A 47 " pdb=" CG TRP A 47 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.30: 121 106.30 - 114.34: 1826 114.34 - 122.38: 2042 122.38 - 130.41: 591 130.41 - 138.45: 13 Bond angle restraints: 4593 Sorted by residual: angle pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sigma weight residual 116.30 138.45 -22.15 3.50e+00 8.16e-02 4.00e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " ideal model delta sigma weight residual 116.20 120.25 -4.05 8.00e-01 1.56e+00 2.57e+01 angle pdb=" N ASN R 477 " pdb=" CA ASN R 477 " pdb=" C ASN R 477 " ideal model delta sigma weight residual 110.97 116.45 -5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 121.31 118.05 3.26 7.40e-01 1.83e+00 1.94e+01 angle pdb=" C LYS B 49 " pdb=" N ASP B 50 " pdb=" CA ASP B 50 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1719 15.93 - 31.86: 193 31.86 - 47.79: 43 47.79 - 63.72: 2 63.72 - 79.64: 4 Dihedral angle restraints: 1961 sinusoidal: 759 harmonic: 1202 Sorted by residual: dihedral pdb=" CA SER B 93 " pdb=" C SER B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 87 " pdb=" CB CYS B 87 " ideal model delta sinusoidal sigma weight residual 93.00 47.57 45.43 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ASP A 105 " pdb=" C ASP A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 1958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 342 0.052 - 0.105: 108 0.105 - 0.157: 42 0.157 - 0.210: 6 0.210 - 0.262: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.18e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.90e+01 chirality pdb=" CB ILE A 19 " pdb=" CA ILE A 19 " pdb=" CG1 ILE A 19 " pdb=" CG2 ILE A 19 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.136 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG C 1 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C VAL A 118 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 118 " -0.026 2.00e-02 2.50e+03 pdb=" N TRP A 119 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 27 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.49e+00 pdb=" N PRO B 28 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.042 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 597 2.76 - 3.30: 2775 3.30 - 3.83: 5395 3.83 - 4.37: 6177 4.37 - 4.90: 11042 Nonbonded interactions: 25986 Sorted by model distance: nonbonded pdb=" NZ LYS R 440 " pdb=" N SER A 104 " model vdw 2.230 3.200 nonbonded pdb=" OG SER R 359 " pdb=" OD1 ASN R 394 " model vdw 2.295 2.440 nonbonded pdb=" O SER B 29 " pdb=" OG SER B 29 " model vdw 2.302 2.440 nonbonded pdb=" NE2 HIS A 35 " pdb=" OD1 ASP A 99 " model vdw 2.307 2.520 nonbonded pdb=" OH TYR B 35 " pdb=" OE1 GLN B 88 " model vdw 2.328 2.440 ... (remaining 25981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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: 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: 9.670 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.008 0.084 3373 Z= 0.558 Angle : 1.160 22.149 4593 Z= 0.630 Chirality : 0.062 0.262 502 Planarity : 0.010 0.111 591 Dihedral : 13.748 79.644 1186 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.48 (0.38), residues: 409 helix: -3.53 (0.89), residues: 21 sheet: -1.93 (0.42), residues: 139 loop : -2.50 (0.36), residues: 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.359 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1445 time to fit residues: 13.0360 Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3373 Z= 0.265 Angle : 0.691 10.419 4593 Z= 0.354 Chirality : 0.046 0.137 502 Planarity : 0.006 0.063 591 Dihedral : 6.169 25.271 465 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.25 (0.39), residues: 409 helix: -3.80 (0.61), residues: 33 sheet: -1.70 (0.42), residues: 144 loop : -2.23 (0.39), residues: 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.410 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 0.1539 time to fit residues: 14.0413 Evaluate side-chains 71 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0338 time to fit residues: 0.7538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3373 Z= 0.242 Angle : 0.633 8.992 4593 Z= 0.323 Chirality : 0.045 0.137 502 Planarity : 0.005 0.049 591 Dihedral : 5.635 21.007 465 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.85 (0.41), residues: 409 helix: -3.96 (0.74), residues: 20 sheet: -1.55 (0.43), residues: 141 loop : -1.96 (0.40), residues: 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.396 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 75 average time/residue: 0.1610 time to fit residues: 14.7632 Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0345 time to fit residues: 0.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 34 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3373 Z= 0.185 Angle : 0.588 6.962 4593 Z= 0.300 Chirality : 0.044 0.134 502 Planarity : 0.005 0.047 591 Dihedral : 5.292 19.923 465 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.42), residues: 409 helix: -4.04 (0.91), residues: 12 sheet: -1.45 (0.44), residues: 141 loop : -1.75 (0.40), residues: 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.396 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.1712 time to fit residues: 14.3455 Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0354 time to fit residues: 0.7887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3373 Z= 0.206 Angle : 0.616 12.068 4593 Z= 0.305 Chirality : 0.044 0.134 502 Planarity : 0.004 0.041 591 Dihedral : 5.190 19.423 465 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.45 (0.43), residues: 409 helix: -4.04 (0.90), residues: 12 sheet: -1.40 (0.45), residues: 141 loop : -1.67 (0.41), residues: 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.401 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.1583 time to fit residues: 12.4864 Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0351 time to fit residues: 0.7311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7583 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 3373 Z= 0.254 Angle : 0.642 10.589 4593 Z= 0.323 Chirality : 0.046 0.219 502 Planarity : 0.004 0.046 591 Dihedral : 5.196 19.804 465 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.65 (0.42), residues: 409 helix: -3.97 (0.68), residues: 20 sheet: -1.42 (0.44), residues: 141 loop : -1.79 (0.41), residues: 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.407 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 0.1463 time to fit residues: 12.1024 Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0355 time to fit residues: 0.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 3373 Z= 0.251 Angle : 0.634 9.885 4593 Z= 0.320 Chirality : 0.045 0.214 502 Planarity : 0.004 0.043 591 Dihedral : 5.198 18.728 465 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.59 (0.42), residues: 409 helix: -3.97 (0.67), residues: 20 sheet: -1.34 (0.45), residues: 141 loop : -1.78 (0.41), residues: 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.398 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 67 average time/residue: 0.1748 time to fit residues: 14.4756 Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7570 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 3373 Z= 0.247 Angle : 0.640 9.046 4593 Z= 0.328 Chirality : 0.046 0.221 502 Planarity : 0.005 0.046 591 Dihedral : 5.242 19.205 465 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.54 (0.42), residues: 409 helix: -3.95 (0.68), residues: 20 sheet: -1.21 (0.45), residues: 135 loop : -1.81 (0.40), residues: 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.394 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1607 time to fit residues: 12.3289 Evaluate side-chains 62 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7555 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 3373 Z= 0.223 Angle : 0.628 8.846 4593 Z= 0.318 Chirality : 0.045 0.189 502 Planarity : 0.004 0.042 591 Dihedral : 5.132 18.908 465 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.50 (0.42), residues: 409 helix: -3.93 (0.68), residues: 20 sheet: -1.04 (0.46), residues: 129 loop : -1.87 (0.40), residues: 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.396 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.1555 time to fit residues: 12.8173 Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0361 time to fit residues: 0.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.4126 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3373 Z= 0.189 Angle : 0.598 7.718 4593 Z= 0.304 Chirality : 0.044 0.163 502 Planarity : 0.004 0.045 591 Dihedral : 4.983 19.158 465 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.51 (0.42), residues: 409 helix: -3.52 (0.96), residues: 14 sheet: -1.00 (0.46), residues: 131 loop : -2.01 (0.39), residues: 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.398 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1529 time to fit residues: 12.9219 Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137970 restraints weight = 3844.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138148 restraints weight = 3223.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139382 restraints weight = 2969.551| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3373 Z= 0.261 Angle : 0.627 8.456 4593 Z= 0.319 Chirality : 0.045 0.169 502 Planarity : 0.004 0.037 591 Dihedral : 5.053 19.180 465 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.63 (0.41), residues: 409 helix: -3.96 (0.67), residues: 20 sheet: -1.17 (0.45), residues: 137 loop : -1.95 (0.40), residues: 252 =============================================================================== Job complete usr+sys time: 1236.29 seconds wall clock time: 22 minutes 46.91 seconds (1366.91 seconds total)