Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:00:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/11_2022/7cah_30331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/11_2022/7cah_30331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/11_2022/7cah_30331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/11_2022/7cah_30331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/11_2022/7cah_30331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/11_2022/7cah_30331.pdb" } resolution = 3.9 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= 0.212 sd= 3.720 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2889 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1282 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 2.22, per 1000 atoms: 0.77 Number of scatterers: 2889 At special positions: 0 Unit cell: (68.64, 72.8, 64.48, 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 7 16.00 O 567 8.00 N 473 7.00 C 1842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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=2.05 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: 1.21 Conformation dependent library (CDL) restraints added in 478.4 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 11.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.717A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.618A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.741A pdb=" N VAL D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.155A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.748A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 96 hydrogen bonds defined for protein. 213 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: 0.74 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 923 1.34 - 1.46: 741 1.46 - 1.58: 1294 1.58 - 1.70: 0 1.70 - 1.82: 7 Bond restraints: 2965 Sorted by residual: bond pdb=" C ILE E 51 " pdb=" N ASP E 52 " ideal model delta sigma weight residual 1.330 1.269 0.061 1.47e-02 4.63e+03 1.73e+01 bond pdb=" C ASP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C THR A 430 " pdb=" N GLY A 431 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.13e-02 7.83e+03 8.60e-01 bond pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.19e-02 7.06e+03 8.56e-01 bond pdb=" CB TRP D 93 " pdb=" CG TRP D 93 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.43e-01 ... (remaining 2960 not shown) Histogram of bond angle deviations from ideal: 102.35 - 109.77: 448 109.77 - 117.19: 1658 117.19 - 124.60: 1897 124.60 - 132.02: 53 132.02 - 139.44: 8 Bond angle restraints: 4064 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS A 378 " pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 123.00 118.23 4.77 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C LYS E 12 " pdb=" N LYS E 13 " pdb=" CA LYS E 13 " ideal model delta sigma weight residual 120.81 139.44 -18.63 5.77e+00 3.00e-02 1.04e+01 angle pdb=" C ILE E 51 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " ideal model delta sigma weight residual 120.68 115.86 4.82 1.52e+00 4.33e-01 1.00e+01 angle pdb=" N HIS A 519 " pdb=" CA HIS A 519 " pdb=" C HIS A 519 " ideal model delta sigma weight residual 114.09 109.34 4.75 1.55e+00 4.16e-01 9.40e+00 ... (remaining 4059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 1503 15.51 - 31.02: 170 31.02 - 46.53: 33 46.53 - 62.04: 1 62.04 - 77.55: 3 Dihedral angle restraints: 1710 sinusoidal: 535 harmonic: 1175 Sorted by residual: dihedral pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N PRO E 103 " pdb=" CA PRO E 103 " ideal model delta harmonic sigma weight residual -180.00 -137.55 -42.45 0 5.00e+00 4.00e-02 7.21e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 1707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 259 0.033 - 0.065: 116 0.065 - 0.098: 48 0.098 - 0.131: 23 0.131 - 0.163: 7 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 450 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO E 103 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 412 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 127 2.69 - 3.24: 3052 3.24 - 3.79: 4383 3.79 - 4.35: 5694 4.35 - 4.90: 9144 Nonbonded interactions: 22400 Sorted by model distance: nonbonded pdb=" OG SER E 119 " pdb=" O ALA E 121 " model vdw 2.137 2.440 nonbonded pdb=" O ASP E 102 " pdb=" N TYR E 104 " model vdw 2.222 2.520 nonbonded pdb=" OD2 ASP E 60 " pdb=" NZ LYS E 65 " model vdw 2.242 2.520 nonbonded pdb=" OD1 ASN A 437 " pdb=" N SER A 438 " model vdw 2.297 2.520 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.336 2.440 ... (remaining 22395 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 7 5.16 5 C 1842 2.51 5 N 473 2.21 5 O 567 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 1.780 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.890 Find NCS groups from input model: 0.080 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 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 : 0.005 0.061 2965 Z= 0.316 Angle : 0.921 18.632 4064 Z= 0.508 Chirality : 0.050 0.163 453 Planarity : 0.006 0.062 531 Dihedral : 13.676 77.553 951 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.95 % Favored : 79.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.53 % 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: -5.76 (0.31), residues: 396 helix: -4.70 (0.25), residues: 39 sheet: -3.12 (0.39), residues: 117 loop : -4.25 (0.30), residues: 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.316 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1171 time to fit residues: 6.5277 Evaluate side-chains 24 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4560 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 2965 Z= 0.186 Angle : 0.712 15.878 4064 Z= 0.359 Chirality : 0.047 0.177 453 Planarity : 0.006 0.059 531 Dihedral : 6.768 41.115 430 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer Outliers : 2.96 % 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: -4.81 (0.34), residues: 396 helix: -3.87 (0.59), residues: 33 sheet: -2.55 (0.41), residues: 119 loop : -3.61 (0.33), residues: 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.0930 time to fit residues: 5.4544 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0247 time to fit residues: 0.5179 ------------------------------------------------------------------------------- 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: 8.9990 chunk 10 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 2965 Z= 0.198 Angle : 0.689 15.023 4064 Z= 0.351 Chirality : 0.047 0.151 453 Planarity : 0.006 0.058 531 Dihedral : 6.577 38.697 430 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer Outliers : 2.59 % 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: -4.52 (0.36), residues: 396 helix: -3.44 (0.57), residues: 39 sheet: -2.37 (0.42), residues: 120 loop : -3.41 (0.35), residues: 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.305 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 42 average time/residue: 0.1235 time to fit residues: 6.7089 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0331 time to fit residues: 0.5860 ------------------------------------------------------------------------------- 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: 0.3980 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 2965 Z= 0.177 Angle : 0.661 13.988 4064 Z= 0.337 Chirality : 0.046 0.145 453 Planarity : 0.006 0.053 531 Dihedral : 6.044 37.024 430 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer Outliers : 3.33 % 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: -4.10 (0.37), residues: 396 helix: -3.60 (0.54), residues: 33 sheet: -2.01 (0.44), residues: 120 loop : -3.11 (0.36), residues: 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 43 average time/residue: 0.1245 time to fit residues: 6.8937 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0311 time to fit residues: 0.6151 ------------------------------------------------------------------------------- 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: 0.0870 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 2965 Z= 0.207 Angle : 0.678 14.395 4064 Z= 0.345 Chirality : 0.046 0.168 453 Planarity : 0.005 0.052 531 Dihedral : 6.152 35.864 430 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer Outliers : 2.59 % 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: -4.00 (0.38), residues: 396 helix: -3.45 (0.59), residues: 33 sheet: -1.90 (0.45), residues: 120 loop : -3.09 (0.37), residues: 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.328 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.1350 time to fit residues: 6.9074 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0359 time to fit residues: 0.6818 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 2965 Z= 0.330 Angle : 0.777 16.203 4064 Z= 0.396 Chirality : 0.049 0.159 453 Planarity : 0.006 0.060 531 Dihedral : 7.163 43.542 430 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.94 % Favored : 81.06 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.27 (0.38), residues: 396 helix: -3.53 (0.54), residues: 33 sheet: -2.06 (0.44), residues: 121 loop : -3.31 (0.36), residues: 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.318 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.1173 time to fit residues: 5.7135 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0352 time to fit residues: 0.6885 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 0.0030 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 30.0000 chunk 25 optimal weight: 0.0040 chunk 18 optimal weight: 0.8980 overall best weight: 1.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2965 Z= 0.194 Angle : 0.687 15.139 4064 Z= 0.348 Chirality : 0.046 0.145 453 Planarity : 0.006 0.058 531 Dihedral : 6.332 40.397 430 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer Outliers : 0.74 % 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: -4.00 (0.38), residues: 396 helix: -3.54 (0.56), residues: 33 sheet: -1.87 (0.45), residues: 119 loop : -3.09 (0.37), residues: 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.1327 time to fit residues: 6.2844 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2525 time to fit residues: 0.6787 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 2965 Z= 0.213 Angle : 0.695 14.794 4064 Z= 0.349 Chirality : 0.046 0.142 453 Planarity : 0.006 0.059 531 Dihedral : 6.301 39.404 430 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer Outliers : 1.48 % 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: -3.86 (0.38), residues: 396 helix: -3.46 (0.59), residues: 33 sheet: -1.74 (0.45), residues: 119 loop : -3.01 (0.37), residues: 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.359 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.1356 time to fit residues: 6.2744 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0421 time to fit residues: 0.5886 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 2965 Z= 0.289 Angle : 0.756 15.556 4064 Z= 0.383 Chirality : 0.048 0.143 453 Planarity : 0.006 0.060 531 Dihedral : 6.763 40.264 430 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % Favored : 82.32 % 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: -4.00 (0.38), residues: 396 helix: -3.41 (0.52), residues: 39 sheet: -1.80 (0.45), residues: 119 loop : -3.12 (0.38), residues: 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1273 time to fit residues: 5.1933 Evaluate side-chains 29 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4898 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2965 Z= 0.176 Angle : 0.668 14.255 4064 Z= 0.336 Chirality : 0.046 0.156 453 Planarity : 0.006 0.056 531 Dihedral : 6.052 38.227 430 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer Outliers : 0.74 % 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: -3.61 (0.40), residues: 396 helix: -3.35 (0.62), residues: 33 sheet: -1.45 (0.46), residues: 121 loop : -2.90 (0.38), residues: 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.335 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.1147 time to fit residues: 5.8856 Evaluate side-chains 29 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4269 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 0.0670 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.092537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.086294 restraints weight = 12353.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.086776 restraints weight = 10748.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.087169 restraints weight = 9631.689| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 2965 Z= 0.189 Angle : 0.726 13.859 4064 Z= 0.358 Chirality : 0.046 0.148 453 Planarity : 0.006 0.056 531 Dihedral : 6.200 36.667 430 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.62 (0.40), residues: 396 helix: -3.12 (0.59), residues: 39 sheet: -1.57 (0.46), residues: 125 loop : -2.87 (0.40), residues: 232 =============================================================================== Job complete usr+sys time: 991.37 seconds wall clock time: 18 minutes 25.48 seconds (1105.48 seconds total)