Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:06:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/11_2022/7mkm_23899.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/11_2022/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/11_2022/7mkm_23899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/11_2022/7mkm_23899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/11_2022/7mkm_23899.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/11_2022/7mkm_23899.pdb" } resolution = 3.16 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1514 Unusual residues: {'NAG': 1} Classifications: {'peptide': 188, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 178, None: 1} Not linked: pdbres="ALA A 520 " pdbres="NAG A 601 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.42, per 1000 atoms: 0.76 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 66.12, 97.44, 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 17 16.00 O 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 475.8 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 12.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 48 through 52 Processing helix chain 'L' and resid 77 through 82 removed outlier: 4.176A pdb=" N ASP L 81 " --> pdb=" O MET L 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.377A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.001A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.182A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.760A pdb=" N PHE H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER H 70 " --> pdb=" O PHE H 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.542A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.634A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.074A pdb=" N ILE L 10 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.572A pdb=" N TYR L 33 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.144A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 78 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1009 1.35 - 1.47: 896 1.47 - 1.58: 1349 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" C TYR A 489 " pdb=" N PHE A 490 " ideal model delta sigma weight residual 1.339 1.413 -0.074 5.57e-02 3.22e+02 1.75e+00 bond pdb=" CG LEU A 387 " pdb=" CD1 LEU A 387 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CG PRO L 94 " pdb=" CD PRO L 94 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.29e-01 bond pdb=" CB ASN A 501 " pdb=" CG ASN A 501 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.26e-01 bond pdb=" CB ASN A 370 " pdb=" CG ASN A 370 " ideal model delta sigma weight residual 1.516 1.533 -0.017 2.50e-02 1.60e+03 4.75e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.45: 95 106.45 - 113.35: 1672 113.35 - 120.25: 1159 120.25 - 127.15: 1492 127.15 - 134.05: 39 Bond angle restraints: 4457 Sorted by residual: angle pdb=" CA ARG L 44 " pdb=" CB ARG L 44 " pdb=" CG ARG L 44 " ideal model delta sigma weight residual 114.10 122.38 -8.28 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CA MET H 64 " pdb=" CB MET H 64 " pdb=" CG MET H 64 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.66e+00 angle pdb=" N LYS A 386 " pdb=" CA LYS A 386 " pdb=" C LYS A 386 " ideal model delta sigma weight residual 112.54 116.98 -4.44 1.51e+00 4.39e-01 8.63e+00 angle pdb=" N SER L 42 " pdb=" CA SER L 42 " pdb=" C SER L 42 " ideal model delta sigma weight residual 109.81 115.50 -5.69 2.21e+00 2.05e-01 6.62e+00 angle pdb=" C ASN A 388 " pdb=" N ASP A 389 " pdb=" CA ASP A 389 " ideal model delta sigma weight residual 122.19 125.81 -3.62 1.41e+00 5.03e-01 6.60e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 1697 16.45 - 32.89: 183 32.89 - 49.34: 28 49.34 - 65.79: 8 65.79 - 82.23: 4 Dihedral angle restraints: 1920 sinusoidal: 743 harmonic: 1177 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 34.95 58.05 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CA TYR L 93 " pdb=" C TYR L 93 " pdb=" N PRO L 94 " pdb=" CA PRO L 94 " ideal model delta harmonic sigma weight residual 0.00 -32.88 32.88 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA ARG L 60 " pdb=" C ARG L 60 " pdb=" N PHE L 61 " pdb=" CA PHE L 61 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 1917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 331 0.044 - 0.088: 102 0.088 - 0.132: 38 0.132 - 0.176: 8 0.176 - 0.220: 1 Chirality restraints: 480 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA VAL H 50 " pdb=" N VAL H 50 " pdb=" C VAL H 50 " pdb=" CB VAL H 50 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 39 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO H 40 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 40 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 40 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.124 9.50e-02 1.11e+02 5.60e-02 2.39e+00 pdb=" NE ARG A 466 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 52 " -0.014 2.00e-02 2.50e+03 9.67e-03 2.34e+00 pdb=" CG TRP H 52 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP H 52 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 52 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 52 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 52 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 52 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 52 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 52 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 52 " -0.005 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 965 2.82 - 3.34: 2804 3.34 - 3.86: 4766 3.86 - 4.38: 5183 4.38 - 4.90: 9054 Nonbonded interactions: 22772 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.304 2.440 nonbonded pdb=" OD1 ASN A 370 " pdb=" N SER A 371 " model vdw 2.323 2.520 nonbonded pdb=" OD1 ASP L 81 " pdb=" N ALA L 82 " model vdw 2.340 2.520 nonbonded pdb=" O VAL L 29 " pdb=" OH TYR L 70 " model vdw 2.358 2.440 nonbonded pdb=" OD2 ASP H 54 " pdb=" ND2 ASN H 73 " model vdw 2.359 2.520 ... (remaining 22767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2030 2.51 5 N 528 2.21 5 O 617 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 5.420 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 13.560 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 3276 Z= 0.222 Angle : 0.789 8.780 4457 Z= 0.414 Chirality : 0.050 0.220 480 Planarity : 0.007 0.056 572 Dihedral : 13.758 82.234 1161 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.82 (0.38), residues: 400 helix: -2.45 (0.81), residues: 13 sheet: 1.62 (0.45), residues: 120 loop : -1.62 (0.33), residues: 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.345 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1541 time to fit residues: 10.4147 Evaluate side-chains 50 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 10 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 3276 Z= 0.177 Angle : 0.684 6.773 4457 Z= 0.357 Chirality : 0.047 0.271 480 Planarity : 0.004 0.039 572 Dihedral : 6.742 23.773 456 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.55 (0.38), residues: 400 helix: -2.23 (0.90), residues: 20 sheet: 1.87 (0.46), residues: 107 loop : -1.26 (0.33), residues: 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.359 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.1511 time to fit residues: 10.1560 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0316 time to fit residues: 0.4919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 3276 Z= 0.371 Angle : 0.804 7.312 4457 Z= 0.429 Chirality : 0.049 0.190 480 Planarity : 0.005 0.041 572 Dihedral : 7.386 28.666 456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.06 (0.36), residues: 400 helix: -1.76 (1.30), residues: 13 sheet: 1.38 (0.44), residues: 109 loop : -1.67 (0.31), residues: 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.366 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.1579 time to fit residues: 11.0299 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0317 time to fit residues: 0.6213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 33 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 3276 Z= 0.240 Angle : 0.690 7.061 4457 Z= 0.364 Chirality : 0.047 0.155 480 Planarity : 0.005 0.040 572 Dihedral : 6.723 23.897 456 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.17 (0.37), residues: 400 helix: -2.55 (0.96), residues: 20 sheet: 1.05 (0.46), residues: 112 loop : -1.56 (0.32), residues: 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.345 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.1440 time to fit residues: 10.3252 Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0366 time to fit residues: 0.5940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 26 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN A 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 3276 Z= 0.213 Angle : 0.649 6.700 4457 Z= 0.345 Chirality : 0.046 0.152 480 Planarity : 0.005 0.039 572 Dihedral : 6.414 28.865 456 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.40 (0.37), residues: 400 helix: -2.46 (0.98), residues: 20 sheet: 0.68 (0.48), residues: 104 loop : -1.57 (0.32), residues: 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.339 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.1513 time to fit residues: 10.9622 Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0432 time to fit residues: 0.6528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3276 Z= 0.231 Angle : 0.667 7.504 4457 Z= 0.357 Chirality : 0.046 0.192 480 Planarity : 0.005 0.033 572 Dihedral : 6.335 23.251 456 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.53 (0.38), residues: 400 helix: -2.49 (0.98), residues: 20 sheet: 0.48 (0.49), residues: 104 loop : -1.61 (0.33), residues: 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.322 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 57 average time/residue: 0.1561 time to fit residues: 11.0042 Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0331 time to fit residues: 0.5779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 3276 Z= 0.335 Angle : 0.771 9.324 4457 Z= 0.408 Chirality : 0.047 0.180 480 Planarity : 0.006 0.060 572 Dihedral : 6.822 25.572 456 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.93 (0.37), residues: 400 helix: -2.52 (0.95), residues: 19 sheet: 0.17 (0.51), residues: 100 loop : -1.89 (0.32), residues: 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.349 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.1882 time to fit residues: 12.1111 Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0389 time to fit residues: 0.7520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.0020 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 3276 Z= 0.207 Angle : 0.694 9.168 4457 Z= 0.359 Chirality : 0.045 0.173 480 Planarity : 0.004 0.034 572 Dihedral : 6.266 28.520 456 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.01 (0.38), residues: 400 helix: -2.83 (0.79), residues: 26 sheet: -0.15 (0.49), residues: 109 loop : -1.79 (0.34), residues: 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.349 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.1593 time to fit residues: 10.3955 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0336 time to fit residues: 0.6220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 3276 Z= 0.215 Angle : 0.697 7.974 4457 Z= 0.360 Chirality : 0.046 0.319 480 Planarity : 0.006 0.104 572 Dihedral : 6.210 30.152 456 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.96 (0.39), residues: 400 helix: -2.81 (0.79), residues: 26 sheet: -0.26 (0.50), residues: 110 loop : -1.69 (0.35), residues: 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.379 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.1635 time to fit residues: 10.4654 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0403 time to fit residues: 0.7230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.0370 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 3276 Z= 0.190 Angle : 0.694 9.468 4457 Z= 0.353 Chirality : 0.045 0.220 480 Planarity : 0.006 0.104 572 Dihedral : 5.908 24.141 456 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.87 (0.39), residues: 400 helix: -2.78 (0.81), residues: 26 sheet: -0.22 (0.50), residues: 110 loop : -1.62 (0.35), residues: 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.321 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.1544 time to fit residues: 9.9300 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0552 time to fit residues: 0.6040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.190551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171350 restraints weight = 5001.329| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.65 r_work: 0.4346 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4338 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.4328 rms_B_bonded: 2.44 restraints_weight: 0.1250 r_work: 0.4318 rms_B_bonded: 2.52 restraints_weight: 0.0625 r_work: 0.4306 rms_B_bonded: 2.65 restraints_weight: 0.0312 r_work: 0.4294 rms_B_bonded: 2.82 restraints_weight: 0.0156 r_work: 0.4281 rms_B_bonded: 3.03 restraints_weight: 0.0078 r_work: 0.4266 rms_B_bonded: 3.28 restraints_weight: 0.0039 r_work: 0.4249 rms_B_bonded: 3.59 restraints_weight: 0.0020 r_work: 0.4230 rms_B_bonded: 3.95 restraints_weight: 0.0010 r_work: 0.4209 rms_B_bonded: 4.39 restraints_weight: 0.0005 r_work: 0.4185 rms_B_bonded: 4.91 restraints_weight: 0.0002 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 3276 Z= 0.233 Angle : 0.711 8.607 4457 Z= 0.366 Chirality : 0.045 0.218 480 Planarity : 0.006 0.100 572 Dihedral : 6.099 23.863 456 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.98 (0.39), residues: 400 helix: -2.80 (0.80), residues: 26 sheet: -0.32 (0.52), residues: 102 loop : -1.65 (0.34), residues: 272 =============================================================================== Job complete usr+sys time: 1176.81 seconds wall clock time: 21 minutes 45.77 seconds (1305.77 seconds total)