Starting phenix.real_space_refine (version: dev) on Mon Apr 4 15:36:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/04_2022/6coy_7544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/04_2022/6coy_7544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/04_2022/6coy_7544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/04_2022/6coy_7544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/04_2022/6coy_7544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/04_2022/6coy_7544.pdb" } resolution = 3.36 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 205": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7156 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3576 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3576 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.51, per 1000 atoms: 0.63 Number of scatterers: 7156 At special positions: 0 Unit cell: (110.21, 77.25, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 58 16.00 O 1188 8.00 N 1130 7.00 C 4776 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: 3.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 78.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 116 through 152 Processing helix chain 'A' and resid 156 through 183 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 299 through 323 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 379 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN A 445 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 475 Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 541 through 551 Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 117 through 152 Processing helix chain 'B' and resid 156 through 183 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 299 through 323 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 347 through 379 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN B 445 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 475 Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'B' and resid 521 through 538 Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'B' and resid 555 through 571 Processing helix chain 'B' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA3, first strand: chain 'B' and resid 510 through 512 551 hydrogen bonds defined for protein. 1551 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: 2.11 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1096 1.31 - 1.43: 2014 1.43 - 1.56: 4140 1.56 - 1.68: 4 1.68 - 1.81: 98 Bond restraints: 7352 Sorted by residual: bond pdb=" CB ILE A 556 " pdb=" CG1 ILE A 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB ILE B 556 " pdb=" CG1 ILE B 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB HIS B 538 " pdb=" CG HIS B 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB HIS A 538 " pdb=" CG HIS A 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB ILE B 553 " pdb=" CG1 ILE B 553 " ideal model delta sigma weight residual 1.530 1.431 0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 7347 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.24: 220 105.24 - 112.41: 3618 112.41 - 119.58: 2560 119.58 - 126.76: 3528 126.76 - 133.93: 80 Bond angle restraints: 10006 Sorted by residual: angle pdb=" C THR B 281 " pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C THR A 281 " pdb=" N PRO A 282 " pdb=" CA PRO A 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C LEU A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C LEU B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C PHE B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 119.56 125.93 -6.37 1.01e+00 9.80e-01 3.97e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4126 17.23 - 34.46: 86 34.46 - 51.69: 18 51.69 - 68.91: 18 68.91 - 86.14: 6 Dihedral angle restraints: 4254 sinusoidal: 1592 harmonic: 2662 Sorted by residual: dihedral pdb=" CA THR B 432 " pdb=" C THR B 432 " pdb=" N TRP B 433 " pdb=" CA TRP B 433 " ideal model delta harmonic sigma weight residual 180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA THR A 432 " pdb=" C THR A 432 " pdb=" N TRP A 433 " pdb=" CA TRP A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" C TYR B 393 " pdb=" N TYR B 393 " pdb=" CA TYR B 393 " pdb=" CB TYR B 393 " ideal model delta harmonic sigma weight residual -122.60 -130.59 7.99 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 4251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 684 0.069 - 0.139: 342 0.139 - 0.208: 102 0.208 - 0.278: 34 0.278 - 0.347: 8 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 407 " pdb=" N PRO B 407 " pdb=" C PRO B 407 " pdb=" CB PRO B 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 558 " pdb=" N PRO B 558 " pdb=" C PRO B 558 " pdb=" CB PRO B 558 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1167 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 590 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO B 591 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 590 " 0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO A 591 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 485 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 486 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 486 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 486 " 0.056 5.00e-02 4.00e+02 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1662 2.77 - 3.31: 7383 3.31 - 3.84: 12334 3.84 - 4.37: 14469 4.37 - 4.90: 24411 Nonbonded interactions: 60259 Sorted by model distance: nonbonded pdb=" N GLN A 185 " pdb=" OE1 GLN A 185 " model vdw 2.242 2.520 nonbonded pdb=" N GLN B 185 " pdb=" OE1 GLN B 185 " model vdw 2.242 2.520 nonbonded pdb=" CB GLU A 291 " pdb=" OE1 GLU A 291 " model vdw 2.449 2.752 nonbonded pdb=" CB GLU B 291 " pdb=" OE1 GLU B 291 " model vdw 2.449 2.752 nonbonded pdb=" OE1 GLU B 291 " pdb=" OG1 THR B 539 " model vdw 2.501 2.440 ... (remaining 60254 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 4 4.86 5 C 4776 2.51 5 N 1130 2.21 5 O 1188 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.020 Extract box with map and model: 7.530 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 23.980 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.020 0.153 7352 Z= 1.323 Angle : 1.425 13.192 10006 Z= 0.978 Chirality : 0.091 0.347 1170 Planarity : 0.014 0.150 1224 Dihedral : 10.542 86.142 2546 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.82 % Favored : 96.75 % 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: -0.30 (0.25), residues: 922 helix: 0.29 (0.18), residues: 668 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1377 time to fit residues: 24.5939 Evaluate side-chains 82 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 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 160 GLN A 436 HIS A 538 HIS B 160 GLN B 436 HIS B 538 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 7352 Z= 0.253 Angle : 0.607 6.511 10006 Z= 0.325 Chirality : 0.043 0.142 1170 Planarity : 0.007 0.070 1224 Dihedral : 4.191 14.994 978 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.31 % 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: 1.86 (0.28), residues: 922 helix: 1.94 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -0.74 (0.42), residues: 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.820 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 134 average time/residue: 0.1556 time to fit residues: 30.0362 Evaluate side-chains 110 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0761 time to fit residues: 1.7986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 74 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 67 optimal weight: 0.7980 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS B 369 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7352 Z= 0.167 Angle : 0.517 6.202 10006 Z= 0.275 Chirality : 0.040 0.139 1170 Planarity : 0.006 0.058 1224 Dihedral : 3.808 13.329 978 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.79 % 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: 2.96 (0.28), residues: 922 helix: 2.81 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.38 (0.42), residues: 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.862 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 104 average time/residue: 0.1472 time to fit residues: 22.8159 Evaluate side-chains 94 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0688 time to fit residues: 1.4758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7352 Z= 0.229 Angle : 0.525 5.689 10006 Z= 0.274 Chirality : 0.041 0.138 1170 Planarity : 0.006 0.059 1224 Dihedral : 3.714 13.925 978 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.31 % 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: 2.87 (0.28), residues: 922 helix: 2.77 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.837 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 112 average time/residue: 0.1478 time to fit residues: 24.4972 Evaluate side-chains 122 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0682 time to fit residues: 2.2750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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: 0.8496 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7352 Z= 0.199 Angle : 0.498 5.794 10006 Z= 0.259 Chirality : 0.041 0.135 1170 Planarity : 0.005 0.054 1224 Dihedral : 3.608 14.876 978 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 2.10 % 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: 3.07 (0.28), residues: 922 helix: 2.90 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.38 (0.41), residues: 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.886 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 0.1527 time to fit residues: 27.7934 Evaluate side-chains 120 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0926 time to fit residues: 2.8266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 7352 Z= 0.235 Angle : 0.521 5.950 10006 Z= 0.272 Chirality : 0.041 0.137 1170 Planarity : 0.005 0.055 1224 Dihedral : 3.611 14.499 978 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.52 % 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: 2.91 (0.28), residues: 922 helix: 2.81 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.896 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.1572 time to fit residues: 26.1120 Evaluate side-chains 108 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0989 time to fit residues: 1.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8519 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7352 Z= 0.220 Angle : 0.510 5.872 10006 Z= 0.266 Chirality : 0.041 0.134 1170 Planarity : 0.005 0.053 1224 Dihedral : 3.595 14.782 978 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.05 % 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: 3.02 (0.28), residues: 922 helix: 2.87 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.43 (0.41), residues: 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.825 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 110 average time/residue: 0.1447 time to fit residues: 23.6497 Evaluate side-chains 112 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0743 time to fit residues: 1.9592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8546 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 7352 Z= 0.271 Angle : 0.540 6.975 10006 Z= 0.281 Chirality : 0.042 0.143 1170 Planarity : 0.005 0.053 1224 Dihedral : 3.646 14.822 978 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.05 % 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: 2.86 (0.28), residues: 922 helix: 2.76 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.816 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 110 average time/residue: 0.1455 time to fit residues: 23.7313 Evaluate side-chains 104 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0709 time to fit residues: 2.1237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.0570 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.8509 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7352 Z= 0.197 Angle : 0.511 6.778 10006 Z= 0.264 Chirality : 0.040 0.136 1170 Planarity : 0.005 0.051 1224 Dihedral : 3.588 15.161 978 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 3.08 (0.28), residues: 922 helix: 2.90 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.36 (0.41), residues: 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.845 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1434 time to fit residues: 21.4096 Evaluate side-chains 103 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8512 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 7352 Z= 0.213 Angle : 0.515 6.602 10006 Z= 0.267 Chirality : 0.041 0.136 1170 Planarity : 0.005 0.052 1224 Dihedral : 3.542 15.040 978 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.79 % 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: 3.04 (0.28), residues: 922 helix: 2.88 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.39 (0.42), residues: 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.848 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 107 average time/residue: 0.1379 time to fit residues: 22.0678 Evaluate side-chains 110 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0855 time to fit residues: 1.7638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.0020 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 75 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.0060 overall best weight: 0.1722 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.125320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107829 restraints weight = 8398.018| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.88 r_work: 0.3089 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.3064 rms_B_bonded: 1.73 restraints_weight: 0.1250 r_work: 0.3050 rms_B_bonded: 1.83 restraints_weight: 0.0625 r_work: 0.3036 rms_B_bonded: 1.96 restraints_weight: 0.0312 r_work: 0.3020 rms_B_bonded: 2.13 restraints_weight: 0.0156 r_work: 0.3003 rms_B_bonded: 2.33 restraints_weight: 0.0078 r_work: 0.2986 rms_B_bonded: 2.57 restraints_weight: 0.0039 r_work: 0.2966 rms_B_bonded: 2.85 restraints_weight: 0.0020 r_work: 0.2945 rms_B_bonded: 3.17 restraints_weight: 0.0010 r_work: 0.2922 rms_B_bonded: 3.53 restraints_weight: 0.0005 r_work: 0.2898 rms_B_bonded: 3.94 restraints_weight: 0.0002 r_work: 0.2871 rms_B_bonded: 4.41 restraints_weight: 0.0001 r_work: 0.2842 rms_B_bonded: 4.93 restraints_weight: 0.0001 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 7352 Z= 0.148 Angle : 0.482 6.460 10006 Z= 0.250 Chirality : 0.039 0.133 1170 Planarity : 0.005 0.050 1224 Dihedral : 3.450 15.802 978 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.26 % 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: 3.42 (0.29), residues: 922 helix: 3.13 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.15 (0.43), residues: 258 =============================================================================== Job complete usr+sys time: 1543.79 seconds wall clock time: 28 minutes 58.97 seconds (1738.97 seconds total)