Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 04:58:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2023/7wwb_32865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2023/7wwb_32865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2023/7wwb_32865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2023/7wwb_32865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2023/7wwb_32865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2023/7wwb_32865_updated.pdb" } resolution = 3.86 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= 0.018 sd= 0.094 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 60 5.16 5 C 3682 2.51 5 N 834 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 591": "OE1" <-> "OE2" Residue "B GLU 591": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5428 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.55, per 1000 atoms: 0.65 Number of scatterers: 5428 At special positions: 0 Unit cell: (107.613, 120.657, 82.612, 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 60 16.00 O 852 8.00 N 834 7.00 C 3682 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: 2.30 Conformation dependent library (CDL) restraints added in 784.0 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 30 through 50 Processing helix chain 'A' and resid 227 through 244 removed outlier: 3.553A pdb=" N ILE A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 233 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 237 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 330 removed outlier: 4.626A pdb=" N LYS A 312 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 314 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 315 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 357 removed outlier: 4.185A pdb=" N VAL A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.656A pdb=" N PHE A 342 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 415 removed outlier: 3.853A pdb=" N VAL A 390 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 391 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 392 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 407 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.578A pdb=" N SER A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE A 455 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 480 through 507 Processing helix chain 'A' and resid 511 through 524 Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 574 through 606 Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 227 through 244 removed outlier: 3.553A pdb=" N ILE B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE B 233 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B 237 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 330 removed outlier: 4.626A pdb=" N LYS B 312 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 314 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 315 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 357 removed outlier: 4.185A pdb=" N VAL B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) Proline residue: B 338 - end of helix removed outlier: 3.656A pdb=" N PHE B 342 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 350 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 415 removed outlier: 3.852A pdb=" N VAL B 390 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 391 " --> pdb=" O HIS B 388 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 392 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE B 395 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 407 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.578A pdb=" N SER B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE B 455 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 480 through 507 Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 574 through 606 392 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 756 1.30 - 1.43: 1504 1.43 - 1.56: 3180 1.56 - 1.68: 34 1.68 - 1.81: 90 Bond restraints: 5564 Sorted by residual: bond pdb=" C GLN B 337 " pdb=" O GLN B 337 " ideal model delta sigma weight residual 1.243 1.177 0.066 9.90e-03 1.02e+04 4.38e+01 bond pdb=" C GLN A 337 " pdb=" O GLN A 337 " ideal model delta sigma weight residual 1.243 1.178 0.065 9.90e-03 1.02e+04 4.35e+01 bond pdb=" C PHE B 339 " pdb=" O PHE B 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" C PHE A 339 " pdb=" O PHE A 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.25e+01 bond pdb=" C17 CLR A 702 " pdb=" C20 CLR A 702 " ideal model delta sigma weight residual 1.535 1.596 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 5559 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.09: 172 107.09 - 113.76: 3164 113.76 - 120.43: 2432 120.43 - 127.11: 1712 127.11 - 133.78: 88 Bond angle restraints: 7568 Sorted by residual: angle pdb=" C PHE B 339 " pdb=" N TRP B 340 " pdb=" CA TRP B 340 " ideal model delta sigma weight residual 120.31 109.51 10.80 1.52e+00 4.33e-01 5.05e+01 angle pdb=" C PHE A 339 " pdb=" N TRP A 340 " pdb=" CA TRP A 340 " ideal model delta sigma weight residual 120.31 109.53 10.78 1.52e+00 4.33e-01 5.03e+01 angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 113.53 107.83 5.70 9.80e-01 1.04e+00 3.38e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 113.53 107.85 5.68 9.80e-01 1.04e+00 3.36e+01 angle pdb=" C PHE B 336 " pdb=" N GLN B 337 " pdb=" CA GLN B 337 " ideal model delta sigma weight residual 120.58 128.05 -7.47 1.32e+00 5.74e-01 3.20e+01 ... (remaining 7563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3110 17.14 - 34.28: 68 34.28 - 51.42: 6 51.42 - 68.56: 4 68.56 - 85.70: 4 Dihedral angle restraints: 3192 sinusoidal: 1238 harmonic: 1954 Sorted by residual: dihedral pdb=" CA TYR B 438 " pdb=" C TYR B 438 " pdb=" N HIS B 439 " pdb=" CA HIS B 439 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 438 " pdb=" C TYR A 438 " pdb=" N HIS A 439 " pdb=" CA HIS A 439 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " pdb=" CD GLU B 591 " pdb=" OE1 GLU B 591 " ideal model delta sinusoidal sigma weight residual 0.00 -85.70 85.70 1 3.00e+01 1.11e-03 9.87e+00 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 642 0.063 - 0.125: 240 0.125 - 0.188: 32 0.188 - 0.251: 8 0.251 - 0.313: 8 Chirality restraints: 930 Sorted by residual: chirality pdb=" C13 CLR A 702 " pdb=" C12 CLR A 702 " pdb=" C14 CLR A 702 " pdb=" C17 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C14 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C15 CLR B 702 " pdb=" C8 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 927 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 343 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C PHE A 343 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 343 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 344 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 343 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C PHE B 343 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE B 343 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 344 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 493 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LEU B 493 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU B 493 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 494 " 0.013 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2831 2.99 - 3.47: 5811 3.47 - 3.94: 8562 3.94 - 4.42: 9849 4.42 - 4.90: 15171 Nonbonded interactions: 42224 Sorted by model distance: nonbonded pdb=" NZ LYS B 326 " pdb=" OD2 ASP B 619 " model vdw 2.511 2.520 nonbonded pdb=" NZ LYS A 326 " pdb=" OD2 ASP A 619 " model vdw 2.512 2.520 nonbonded pdb=" O CYS B 26 " pdb=" OG1 THR B 27 " model vdw 2.531 2.440 nonbonded pdb=" O CYS A 26 " pdb=" OG1 THR A 27 " model vdw 2.531 2.440 nonbonded pdb=" N PHE B 336 " pdb=" N GLN B 337 " model vdw 2.561 2.560 ... (remaining 42219 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 2.570 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 0.066 5564 Z= 0.527 Angle : 0.969 10.801 7568 Z= 0.650 Chirality : 0.066 0.313 930 Planarity : 0.006 0.026 860 Dihedral : 9.509 85.703 1916 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: 0.18 (0.31), residues: 642 helix: 0.69 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -2.08 (0.51), residues: 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1857 time to fit residues: 67.5443 Evaluate side-chains 169 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 330 HIS A 466 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5564 Z= 0.193 Angle : 0.648 7.430 7568 Z= 0.337 Chirality : 0.037 0.148 930 Planarity : 0.007 0.028 860 Dihedral : 5.221 41.307 724 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 6.21 % 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: 0.39 (0.31), residues: 642 helix: 0.72 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.61 (0.54), residues: 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 208 average time/residue: 0.1867 time to fit residues: 51.1684 Evaluate side-chains 180 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0594 time to fit residues: 3.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 403 GLN B 439 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5564 Z= 0.171 Angle : 0.582 6.868 7568 Z= 0.303 Chirality : 0.036 0.171 930 Planarity : 0.005 0.029 860 Dihedral : 5.111 38.931 724 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 2.52 % 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: -0.02 (0.32), residues: 642 helix: 0.47 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.93 (0.52), residues: 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 185 average time/residue: 0.1511 time to fit residues: 36.6540 Evaluate side-chains 159 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0500 time to fit residues: 1.3435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 439 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5564 Z= 0.220 Angle : 0.625 8.785 7568 Z= 0.319 Chirality : 0.038 0.152 930 Planarity : 0.005 0.027 860 Dihedral : 5.237 41.651 724 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 3.36 % 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: -0.37 (0.32), residues: 642 helix: 0.26 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -2.28 (0.51), residues: 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 172 average time/residue: 0.1595 time to fit residues: 36.5493 Evaluate side-chains 167 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0550 time to fit residues: 2.4108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 5564 Z= 0.237 Angle : 0.625 7.822 7568 Z= 0.322 Chirality : 0.038 0.195 930 Planarity : 0.005 0.036 860 Dihedral : 5.416 44.357 724 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.11 % Rotamer Outliers : 2.85 % 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: -0.42 (0.32), residues: 642 helix: 0.20 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.26 (0.56), residues: 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 0.572 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 172 average time/residue: 0.1368 time to fit residues: 31.5343 Evaluate side-chains 159 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0520 time to fit residues: 1.6144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 61 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7810 moved from start: 0.7218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5564 Z= 0.160 Angle : 0.584 7.441 7568 Z= 0.301 Chirality : 0.036 0.191 930 Planarity : 0.005 0.026 860 Dihedral : 5.196 46.486 724 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.84 % 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: -0.28 (0.33), residues: 642 helix: 0.29 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.26 (0.57), residues: 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 165 average time/residue: 0.1327 time to fit residues: 29.8596 Evaluate side-chains 152 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0546 time to fit residues: 1.0674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5564 Z= 0.171 Angle : 0.608 8.829 7568 Z= 0.311 Chirality : 0.037 0.189 930 Planarity : 0.005 0.026 860 Dihedral : 5.121 49.675 724 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer Outliers : 1.51 % 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: -0.15 (0.33), residues: 642 helix: 0.37 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.10 (0.57), residues: 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 158 average time/residue: 0.1430 time to fit residues: 30.3371 Evaluate side-chains 144 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0519 time to fit residues: 1.1374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5564 Z= 0.192 Angle : 0.638 7.865 7568 Z= 0.325 Chirality : 0.038 0.192 930 Planarity : 0.005 0.026 860 Dihedral : 5.230 54.115 724 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.64 % Rotamer Outliers : 1.34 % 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: -0.15 (0.33), residues: 642 helix: 0.35 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.02 (0.58), residues: 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 159 average time/residue: 0.1695 time to fit residues: 35.5537 Evaluate side-chains 150 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0687 time to fit residues: 1.4368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5564 Z= 0.210 Angle : 0.667 7.985 7568 Z= 0.336 Chirality : 0.039 0.214 930 Planarity : 0.005 0.026 860 Dihedral : 5.334 59.964 724 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.52 % Favored : 95.17 % Rotamer Outliers : 1.17 % 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: -0.17 (0.33), residues: 642 helix: 0.38 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.14 (0.56), residues: 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 166 average time/residue: 0.1510 time to fit residues: 33.3764 Evaluate side-chains 157 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0536 time to fit residues: 1.3037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.8012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5564 Z= 0.198 Angle : 0.675 9.897 7568 Z= 0.340 Chirality : 0.038 0.229 930 Planarity : 0.005 0.032 860 Dihedral : 5.319 56.401 724 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.36 % Favored : 95.33 % Rotamer Outliers : 1.17 % 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: -0.15 (0.33), residues: 642 helix: 0.43 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.26 (0.55), residues: 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 158 average time/residue: 0.1482 time to fit residues: 31.4020 Evaluate side-chains 156 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0574 time to fit residues: 1.1692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114907 restraints weight = 9435.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117920 restraints weight = 6204.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119890 restraints weight = 4836.287| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.8098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 5564 Z= 0.233 Angle : 0.713 9.733 7568 Z= 0.357 Chirality : 0.040 0.234 930 Planarity : 0.005 0.033 860 Dihedral : 5.422 53.698 724 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.83 % Favored : 94.86 % Rotamer Outliers : 0.50 % 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: -0.23 (0.33), residues: 642 helix: 0.41 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -2.40 (0.53), residues: 118 =============================================================================== Job complete usr+sys time: 1325.58 seconds wall clock time: 24 minutes 39.07 seconds (1479.07 seconds total)