Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:42:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/11_2022/7kwz_23059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/11_2022/7kwz_23059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/11_2022/7kwz_23059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/11_2022/7kwz_23059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/11_2022/7kwz_23059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwz_23059/11_2022/7kwz_23059.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped 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: 4695 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "B" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 939 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Time building chain proxies: 2.95, per 1000 atoms: 0.63 Number of scatterers: 4695 At special positions: 0 Unit cell: (94.392, 91.08, 52.992, 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 50 16.00 O 980 8.00 N 895 7.00 C 2770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 685.5 milliseconds 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 29.30 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 865 1.31 - 1.43: 1405 1.43 - 1.56: 2415 1.56 - 1.68: 0 1.68 - 1.80: 100 Bond restraints: 4785 Sorted by residual: bond pdb=" CB ASN D 319 " pdb=" CG ASN D 319 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.82e+00 bond pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.76e+00 bond pdb=" CB ASN C 319 " pdb=" CG ASN C 319 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.70e+00 bond pdb=" CB ASN E 319 " pdb=" CG ASN E 319 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.65e+00 bond pdb=" CB ASN B 319 " pdb=" CG ASN B 319 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.65e+00 ... (remaining 4780 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.50: 110 105.50 - 112.66: 2018 112.66 - 119.82: 1558 119.82 - 126.99: 2635 126.99 - 134.15: 64 Bond angle restraints: 6385 Sorted by residual: angle pdb=" C MET D 336 " pdb=" N MET D 337 " pdb=" CA MET D 337 " ideal model delta sigma weight residual 122.17 117.93 4.24 1.54e+00 4.22e-01 7.57e+00 angle pdb=" C MET C 336 " pdb=" N MET C 337 " pdb=" CA MET C 337 " ideal model delta sigma weight residual 122.17 117.96 4.21 1.54e+00 4.22e-01 7.47e+00 angle pdb=" C MET A 336 " pdb=" N MET A 337 " pdb=" CA MET A 337 " ideal model delta sigma weight residual 122.17 117.99 4.18 1.54e+00 4.22e-01 7.36e+00 angle pdb=" C MET B 336 " pdb=" N MET B 337 " pdb=" CA MET B 337 " ideal model delta sigma weight residual 122.17 117.99 4.18 1.54e+00 4.22e-01 7.36e+00 angle pdb=" C MET E 336 " pdb=" N MET E 337 " pdb=" CA MET E 337 " ideal model delta sigma weight residual 122.17 118.01 4.16 1.54e+00 4.22e-01 7.31e+00 ... (remaining 6380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.30: 2119 9.30 - 18.60: 281 18.60 - 27.90: 181 27.90 - 37.20: 59 37.20 - 46.50: 15 Dihedral angle restraints: 2655 sinusoidal: 940 harmonic: 1715 Sorted by residual: dihedral pdb=" CA MET C 337 " pdb=" C MET C 337 " pdb=" N GLY C 338 " pdb=" CA GLY C 338 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA MET E 337 " pdb=" C MET E 337 " pdb=" N GLY E 338 " pdb=" CA GLY E 338 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA MET A 337 " pdb=" C MET A 337 " pdb=" N GLY A 338 " pdb=" CA GLY A 338 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 2652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 251 0.027 - 0.054: 167 0.054 - 0.081: 57 0.081 - 0.108: 37 0.108 - 0.135: 23 Chirality restraints: 535 Sorted by residual: chirality pdb=" CA ILE C 318 " pdb=" N ILE C 318 " pdb=" C ILE C 318 " pdb=" CB ILE C 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 532 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 319 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C ASN D 319 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN D 319 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO D 320 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 319 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C ASN E 319 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN E 319 " -0.007 2.00e-02 2.50e+03 pdb=" N PRO E 320 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 319 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C ASN A 319 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN A 319 " -0.007 2.00e-02 2.50e+03 pdb=" N PRO A 320 " -0.007 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1365 2.80 - 3.32: 4508 3.32 - 3.85: 8023 3.85 - 4.37: 9905 4.37 - 4.90: 19033 Nonbonded interactions: 42834 Sorted by model distance: nonbonded pdb=" O ASN C 279 " pdb=" OD1 ASN D 279 " model vdw 2.271 3.040 nonbonded pdb=" O ASN D 279 " pdb=" OD1 ASN E 279 " model vdw 2.276 3.040 nonbonded pdb=" O ASN B 279 " pdb=" OD1 ASN C 279 " model vdw 2.285 3.040 nonbonded pdb=" O ASN A 279 " pdb=" OD1 ASN B 279 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 374 " pdb=" O GLY C 351 " model vdw 2.310 2.440 ... (remaining 42829 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 50 5.16 5 C 2770 2.51 5 N 895 2.21 5 O 980 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: 0.310 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: 2.060 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.190 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.006 0.060 4785 Z= 0.299 Angle : 0.804 6.384 6385 Z= 0.436 Chirality : 0.048 0.135 535 Planarity : 0.003 0.027 940 Dihedral : 12.477 46.502 1635 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % 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: -5.51 (0.15), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.11), residues: 685 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1578 time to fit residues: 25.9522 Evaluate side-chains 77 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 344 GLN B 360 GLN ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 344 GLN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 4785 Z= 0.156 Angle : 0.678 6.910 6385 Z= 0.346 Chirality : 0.044 0.119 535 Planarity : 0.002 0.031 940 Dihedral : 5.425 23.395 705 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 3.64 % 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: -5.38 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.499 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.1652 time to fit residues: 21.5285 Evaluate side-chains 88 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0483 time to fit residues: 1.6569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 16 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 4785 Z= 0.223 Angle : 0.695 6.715 6385 Z= 0.358 Chirality : 0.044 0.128 535 Planarity : 0.004 0.048 940 Dihedral : 5.478 25.745 705 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.33 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.495 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 95 average time/residue: 0.1723 time to fit residues: 20.6038 Evaluate side-chains 88 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0493 time to fit residues: 0.9973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 28 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 4785 Z= 0.239 Angle : 0.724 6.702 6385 Z= 0.370 Chirality : 0.044 0.126 535 Planarity : 0.004 0.050 940 Dihedral : 5.451 25.957 705 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer Outliers : 0.91 % 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: -5.31 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.554 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 87 average time/residue: 0.1620 time to fit residues: 18.1198 Evaluate side-chains 81 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0552 time to fit residues: 0.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.2980 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.027 4785 Z= 0.267 Angle : 0.756 7.217 6385 Z= 0.388 Chirality : 0.045 0.140 535 Planarity : 0.004 0.057 940 Dihedral : 5.548 26.602 705 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.40 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.493 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 89 average time/residue: 0.1651 time to fit residues: 18.7614 Evaluate side-chains 82 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0663 time to fit residues: 0.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4785 Z= 0.191 Angle : 0.710 7.798 6385 Z= 0.362 Chirality : 0.044 0.121 535 Planarity : 0.004 0.067 940 Dihedral : 5.245 24.490 705 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.411 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 84 average time/residue: 0.1593 time to fit residues: 17.2078 Evaluate side-chains 80 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 0.0470 chunk 62 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.037 4785 Z= 0.341 Angle : 0.817 9.226 6385 Z= 0.423 Chirality : 0.046 0.162 535 Planarity : 0.005 0.072 940 Dihedral : 5.790 27.069 705 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.06 % Favored : 83.94 % Rotamer Outliers : 1.59 % 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: -5.54 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.496 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 94 average time/residue: 0.1635 time to fit residues: 19.5981 Evaluate side-chains 88 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0464 time to fit residues: 0.9022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4785 Z= 0.156 Angle : 0.684 6.983 6385 Z= 0.356 Chirality : 0.044 0.137 535 Planarity : 0.005 0.073 940 Dihedral : 5.059 22.505 705 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 0.91 % 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: -5.42 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.489 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 90 average time/residue: 0.1564 time to fit residues: 18.2356 Evaluate side-chains 83 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4785 Z= 0.268 Angle : 0.771 6.908 6385 Z= 0.404 Chirality : 0.045 0.124 535 Planarity : 0.005 0.076 940 Dihedral : 5.454 25.426 705 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer Outliers : 0.68 % 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: -5.51 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.12), residues: 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.509 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 81 average time/residue: 0.1652 time to fit residues: 17.2264 Evaluate side-chains 80 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0564 time to fit residues: 0.8300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 chunk 54 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 0.0470 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 4785 Z= 0.140 Angle : 0.700 8.258 6385 Z= 0.364 Chirality : 0.044 0.151 535 Planarity : 0.005 0.079 940 Dihedral : 4.920 22.222 705 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % 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: -5.35 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.12), residues: 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.516 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1546 time to fit residues: 17.1669 Evaluate side-chains 82 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 2 optimal weight: 0.0000 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 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 = 0.4200 r_free = 0.4200 target = 0.133580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092264 restraints weight = 6051.618| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.77 r_work: 0.3638 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work: 0.3613 rms_B_bonded: 2.55 restraints_weight: 0.1250 r_work: 0.3600 rms_B_bonded: 2.61 restraints_weight: 0.0625 r_work: 0.3586 rms_B_bonded: 2.69 restraints_weight: 0.0312 r_work: 0.3571 rms_B_bonded: 2.81 restraints_weight: 0.0156 r_work: 0.3555 rms_B_bonded: 2.95 restraints_weight: 0.0078 r_work: 0.3539 rms_B_bonded: 3.12 restraints_weight: 0.0039 r_work: 0.3521 rms_B_bonded: 3.33 restraints_weight: 0.0020 r_work: 0.3502 rms_B_bonded: 3.57 restraints_weight: 0.0010 r_work: 0.3481 rms_B_bonded: 3.85 restraints_weight: 0.0005 r_work: 0.3459 rms_B_bonded: 4.17 restraints_weight: 0.0002 r_work: 0.3435 rms_B_bonded: 4.55 restraints_weight: 0.0001 r_work: 0.3410 rms_B_bonded: 4.97 restraints_weight: 0.0001 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 4785 Z= 0.405 Angle : 0.890 9.685 6385 Z= 0.467 Chirality : 0.048 0.154 535 Planarity : 0.006 0.083 940 Dihedral : 5.891 28.655 705 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer Outliers : 0.91 % 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: -5.58 (0.16), residues: 685 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.12), residues: 685 =============================================================================== Job complete usr+sys time: 1292.59 seconds wall clock time: 24 minutes 30.07 seconds (1470.07 seconds total)