Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 13:32:19 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/12_2021/6y5l_10701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/12_2021/6y5l_10701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/12_2021/6y5l_10701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/12_2021/6y5l_10701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/12_2021/6y5l_10701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/12_2021/6y5l_10701.pdb" } resolution = 3.6 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= 0.004 sd= 0.140 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 531 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 740 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 531 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain breaks: 1 Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 531 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain breaks: 1 Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 740 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "F" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 740 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.69 Number of scatterers: 3855 At special positions: 0 Unit cell: (68.481, 71.742, 147.832, 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 12 16.00 O 786 8.00 N 654 7.00 C 2403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG C 401 " - " ASN C 38 " " NAG E 401 " - " ASN E 38 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 710.1 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 55.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 38 through 125 Processing helix chain 'D' and resid 38 through 125 Processing helix chain 'F' and resid 38 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA5, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AA6, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AA7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AA9, first strand: chain 'E' and resid 294 through 295 273 hydrogen bonds defined for protein. 792 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: 0.96 Time building geometry restraints manager: 1.62 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: 1270 1.34 - 1.46: 370 1.46 - 1.57: 2242 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 3900 Sorted by residual: bond pdb=" CG ASP D 112 " pdb=" OD1 ASP D 112 " ideal model delta sigma weight residual 1.249 1.231 0.018 1.90e-02 2.77e+03 9.21e-01 bond pdb=" CB ILE B 66 " pdb=" CG2 ILE B 66 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.15e-01 bond pdb=" CB GLN E 311 " pdb=" CG GLN E 311 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.13e-01 bond pdb=" CB ILE F 66 " pdb=" CG2 ILE F 66 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.07e-01 bond pdb=" CB ILE D 66 " pdb=" CG2 ILE D 66 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.91e-01 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 100.91 - 107.53: 114 107.53 - 114.15: 2324 114.15 - 120.77: 1633 120.77 - 127.39: 1179 127.39 - 134.01: 21 Bond angle restraints: 5271 Sorted by residual: angle pdb=" N ILE E 29 " pdb=" CA ILE E 29 " pdb=" C ILE E 29 " ideal model delta sigma weight residual 112.96 110.20 2.76 1.00e+00 1.00e+00 7.60e+00 angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 112.96 110.22 2.74 1.00e+00 1.00e+00 7.50e+00 angle pdb=" N ILE A 29 " pdb=" CA ILE A 29 " pdb=" C ILE A 29 " ideal model delta sigma weight residual 112.96 110.23 2.73 1.00e+00 1.00e+00 7.47e+00 angle pdb=" N ALA E 317 " pdb=" CA ALA E 317 " pdb=" C ALA E 317 " ideal model delta sigma weight residual 110.42 114.10 -3.68 1.46e+00 4.69e-01 6.35e+00 angle pdb=" N ALA A 317 " pdb=" CA ALA A 317 " pdb=" C ALA A 317 " ideal model delta sigma weight residual 110.42 114.05 -3.63 1.46e+00 4.69e-01 6.18e+00 ... (remaining 5266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2169 17.34 - 34.67: 204 34.67 - 52.01: 48 52.01 - 69.35: 6 69.35 - 86.69: 3 Dihedral angle restraints: 2430 sinusoidal: 1032 harmonic: 1398 Sorted by residual: dihedral pdb=" CA PRO C 306 " pdb=" C PRO C 306 " pdb=" N LYS C 307 " pdb=" CA LYS C 307 " ideal model delta harmonic sigma weight residual -180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PRO A 306 " pdb=" C PRO A 306 " pdb=" N LYS A 307 " pdb=" CA LYS A 307 " ideal model delta harmonic sigma weight residual -180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PRO E 306 " pdb=" C PRO E 306 " pdb=" N LYS E 307 " pdb=" CA LYS E 307 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 349 0.028 - 0.057: 151 0.057 - 0.085: 64 0.085 - 0.113: 37 0.113 - 0.141: 26 Chirality restraints: 627 Sorted by residual: chirality pdb=" CA ASP F 46 " pdb=" N ASP F 46 " pdb=" C ASP F 46 " pdb=" CB ASP F 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ASP B 46 " pdb=" N ASP B 46 " pdb=" C ASP B 46 " pdb=" CB ASP B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ASP D 46 " pdb=" N ASP D 46 " pdb=" C ASP D 46 " pdb=" CB ASP D 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 624 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 46 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" CG ASP B 46 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP B 46 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 46 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 46 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" CG ASP F 46 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP F 46 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 46 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 46 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" CG ASP D 46 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 46 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP D 46 " 0.016 2.00e-02 2.50e+03 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 163 2.71 - 3.26: 4084 3.26 - 3.80: 5948 3.80 - 4.35: 6904 4.35 - 4.90: 11814 Nonbonded interactions: 28913 Sorted by model distance: nonbonded pdb=" NZ LYS A 27 " pdb=" OE2 GLU B 97 " model vdw 2.161 2.520 nonbonded pdb=" NZ LYS E 27 " pdb=" OE2 GLU F 97 " model vdw 2.259 2.520 nonbonded pdb=" NZ LYS C 27 " pdb=" OE2 GLU D 97 " model vdw 2.388 2.520 nonbonded pdb=" O LEU D 38 " pdb=" OG1 THR D 41 " model vdw 2.400 2.440 nonbonded pdb=" O LEU B 38 " pdb=" OG1 THR B 41 " model vdw 2.400 2.440 ... (remaining 28908 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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 12 5.16 5 C 2403 2.51 5 N 654 2.21 5 O 786 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.430 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.380 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3900 Z= 0.200 Angle : 0.687 6.830 5271 Z= 0.399 Chirality : 0.048 0.141 627 Planarity : 0.006 0.051 684 Dihedral : 14.519 86.685 1503 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % 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: -2.14 (0.34), residues: 459 helix: 0.80 (0.25), residues: 261 sheet: -4.11 (0.66), residues: 30 loop : -4.75 (0.34), residues: 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1818 time to fit residues: 43.3523 Evaluate side-chains 164 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 60 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 322 ASN D 53 ASN D 60 ASN D 78 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 3900 Z= 0.295 Angle : 0.704 4.985 5271 Z= 0.378 Chirality : 0.047 0.150 627 Planarity : 0.005 0.041 684 Dihedral : 5.613 37.243 516 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 5.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.38), residues: 459 helix: 2.43 (0.26), residues: 261 sheet: -4.35 (0.44), residues: 30 loop : -4.43 (0.37), residues: 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 174 average time/residue: 0.1881 time to fit residues: 38.5460 Evaluate side-chains 171 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0384 time to fit residues: 1.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN E 322 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 3900 Z= 0.322 Angle : 0.785 13.466 5271 Z= 0.409 Chirality : 0.047 0.150 627 Planarity : 0.006 0.044 684 Dihedral : 5.559 36.705 516 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.40), residues: 459 helix: 2.91 (0.27), residues: 261 sheet: -4.26 (0.48), residues: 30 loop : -4.25 (0.39), residues: 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 171 average time/residue: 0.1807 time to fit residues: 36.4554 Evaluate side-chains 158 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0765 time to fit residues: 1.3846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0010 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3900 Z= 0.222 Angle : 0.771 12.764 5271 Z= 0.410 Chirality : 0.045 0.181 627 Planarity : 0.005 0.046 684 Dihedral : 5.276 36.498 516 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.40), residues: 459 helix: 3.14 (0.28), residues: 261 sheet: -3.98 (0.54), residues: 30 loop : -4.00 (0.39), residues: 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 155 average time/residue: 0.1792 time to fit residues: 32.9982 Evaluate side-chains 160 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0612 time to fit residues: 1.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 322 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 3900 Z= 0.384 Angle : 0.880 12.122 5271 Z= 0.464 Chirality : 0.051 0.174 627 Planarity : 0.006 0.046 684 Dihedral : 5.592 36.852 516 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.39), residues: 459 helix: 2.72 (0.28), residues: 261 sheet: -3.74 (0.60), residues: 30 loop : -4.01 (0.40), residues: 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 170 average time/residue: 0.1820 time to fit residues: 36.6254 Evaluate side-chains 160 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1269 time to fit residues: 1.0937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 4 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3900 Z= 0.251 Angle : 0.844 13.389 5271 Z= 0.444 Chirality : 0.047 0.181 627 Planarity : 0.006 0.043 684 Dihedral : 5.440 37.099 516 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.40), residues: 459 helix: 2.68 (0.29), residues: 261 sheet: -3.63 (0.63), residues: 30 loop : -3.89 (0.40), residues: 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 164 average time/residue: 0.1788 time to fit residues: 34.7417 Evaluate side-chains 156 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0400 time to fit residues: 1.0991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 3900 Z= 0.301 Angle : 0.905 14.509 5271 Z= 0.480 Chirality : 0.049 0.201 627 Planarity : 0.006 0.045 684 Dihedral : 5.506 36.930 516 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.40), residues: 459 helix: 2.51 (0.28), residues: 261 sheet: -3.49 (0.67), residues: 30 loop : -3.91 (0.41), residues: 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 163 average time/residue: 0.1779 time to fit residues: 34.3367 Evaluate side-chains 158 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1257 time to fit residues: 1.5021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 3900 Z= 0.311 Angle : 0.935 14.751 5271 Z= 0.499 Chirality : 0.050 0.197 627 Planarity : 0.006 0.045 684 Dihedral : 5.523 36.982 516 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.40), residues: 459 helix: 2.41 (0.29), residues: 261 sheet: -3.38 (0.72), residues: 30 loop : -3.84 (0.42), residues: 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 156 average time/residue: 0.1839 time to fit residues: 34.2386 Evaluate side-chains 150 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0345 time to fit residues: 0.8509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 3 optimal weight: 0.0370 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN C 322 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3900 Z= 0.258 Angle : 0.972 15.984 5271 Z= 0.515 Chirality : 0.051 0.216 627 Planarity : 0.006 0.045 684 Dihedral : 5.288 36.807 516 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.39), residues: 459 helix: 2.33 (0.29), residues: 261 sheet: -3.38 (0.72), residues: 30 loop : -3.74 (0.41), residues: 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 149 average time/residue: 0.1904 time to fit residues: 33.7285 Evaluate side-chains 148 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3077 time to fit residues: 0.9975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 3900 Z= 0.290 Angle : 1.030 16.997 5271 Z= 0.551 Chirality : 0.053 0.224 627 Planarity : 0.006 0.045 684 Dihedral : 5.369 37.119 516 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.39), residues: 459 helix: 2.15 (0.29), residues: 261 sheet: -3.25 (0.74), residues: 30 loop : -3.63 (0.42), residues: 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 151 average time/residue: 0.1799 time to fit residues: 32.1729 Evaluate side-chains 146 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0323 time to fit residues: 0.6894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.128139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089359 restraints weight = 7052.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091574 restraints weight = 4856.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092818 restraints weight = 3933.713| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 3900 Z= 0.309 Angle : 1.054 17.767 5271 Z= 0.555 Chirality : 0.053 0.226 627 Planarity : 0.006 0.044 684 Dihedral : 5.448 37.410 516 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.39), residues: 459 helix: 2.13 (0.29), residues: 261 sheet: -3.15 (0.78), residues: 30 loop : -3.56 (0.43), residues: 168 =============================================================================== Job complete usr+sys time: 1370.98 seconds wall clock time: 25 minutes 22.15 seconds (1522.15 seconds total)