Starting phenix.real_space_refine on Mon Nov 13 15:51:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/11_2023/7q67_13854.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/11_2023/7q67_13854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/11_2023/7q67_13854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/11_2023/7q67_13854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/11_2023/7q67_13854.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/11_2023/7q67_13854.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1639 2.51 5 N 440 2.21 5 O 539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 2618 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "D" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "F" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "H" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "I" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "J" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "K" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Time building chain proxies: 1.55, per 1000 atoms: 0.59 Number of scatterers: 2618 At special positions: 0 Unit cell: (88.2, 49.35, 44.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 539 8.00 N 440 7.00 C 1639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 530.6 milliseconds 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 616 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 109 removed outlier: 7.008A pdb=" N ALA A 107 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN C 108 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 109 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA C 107 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN E 108 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN C 109 " --> pdb=" O GLN E 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA E 107 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN G 108 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 109 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA G 107 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN I 108 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN G 109 " --> pdb=" O GLN I 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA I 107 " --> pdb=" O PHE K 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN K 108 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN I 109 " --> pdb=" O GLN K 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 109 removed outlier: 7.008A pdb=" N ALA B 107 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN D 108 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN B 109 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA D 107 " --> pdb=" O PHE F 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN F 108 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 109 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA F 107 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN H 108 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN F 109 " --> pdb=" O GLN H 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA H 107 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN J 108 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN H 109 " --> pdb=" O GLN J 108 " (cutoff:3.500A) 27 hydrogen bonds defined for protein. 81 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: 0.51 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 429 1.27 - 1.33: 382 1.33 - 1.40: 379 1.40 - 1.47: 522 1.47 - 1.54: 961 Bond restraints: 2673 Sorted by residual: bond pdb=" CA PHE I 114 " pdb=" CB PHE I 114 " ideal model delta sigma weight residual 1.530 1.485 0.045 1.58e-02 4.01e+03 8.10e+00 bond pdb=" CA PHE E 114 " pdb=" CB PHE E 114 " ideal model delta sigma weight residual 1.530 1.486 0.045 1.58e-02 4.01e+03 7.99e+00 bond pdb=" CA PHE K 114 " pdb=" CB PHE K 114 " ideal model delta sigma weight residual 1.530 1.486 0.045 1.58e-02 4.01e+03 7.98e+00 bond pdb=" CA PHE C 114 " pdb=" CB PHE C 114 " ideal model delta sigma weight residual 1.530 1.486 0.045 1.58e-02 4.01e+03 7.98e+00 bond pdb=" CA PHE B 114 " pdb=" CB PHE B 114 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.58e-02 4.01e+03 7.91e+00 ... (remaining 2668 not shown) Histogram of bond angle deviations from ideal: 100.32 - 106.71: 99 106.71 - 113.09: 1221 113.09 - 119.47: 797 119.47 - 125.86: 1436 125.86 - 132.24: 55 Bond angle restraints: 3608 Sorted by residual: angle pdb=" N PHE F 114 " pdb=" CA PHE F 114 " pdb=" CB PHE F 114 " ideal model delta sigma weight residual 109.82 100.32 9.50 1.52e+00 4.33e-01 3.90e+01 angle pdb=" N PHE D 114 " pdb=" CA PHE D 114 " pdb=" CB PHE D 114 " ideal model delta sigma weight residual 109.82 100.34 9.48 1.52e+00 4.33e-01 3.89e+01 angle pdb=" N PHE A 114 " pdb=" CA PHE A 114 " pdb=" CB PHE A 114 " ideal model delta sigma weight residual 109.82 100.34 9.48 1.52e+00 4.33e-01 3.89e+01 angle pdb=" N PHE G 114 " pdb=" CA PHE G 114 " pdb=" CB PHE G 114 " ideal model delta sigma weight residual 109.82 100.35 9.47 1.52e+00 4.33e-01 3.88e+01 angle pdb=" N PHE B 114 " pdb=" CA PHE B 114 " pdb=" CB PHE B 114 " ideal model delta sigma weight residual 109.82 100.35 9.47 1.52e+00 4.33e-01 3.88e+01 ... (remaining 3603 not shown) Histogram of dihedral angle deviations from ideal: 0.05 - 8.42: 1024 8.42 - 16.80: 263 16.80 - 25.17: 99 25.17 - 33.54: 44 33.54 - 41.92: 33 Dihedral angle restraints: 1463 sinusoidal: 495 harmonic: 968 Sorted by residual: dihedral pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" N PHE E 114 " pdb=" CA PHE E 114 " ideal model delta harmonic sigma weight residual -180.00 -138.08 -41.92 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA GLY J 113 " pdb=" C GLY J 113 " pdb=" N PHE J 114 " pdb=" CA PHE J 114 " ideal model delta harmonic sigma weight residual -180.00 -138.09 -41.91 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA GLY G 113 " pdb=" C GLY G 113 " pdb=" N PHE G 114 " pdb=" CA PHE G 114 " ideal model delta harmonic sigma weight residual 180.00 -138.09 -41.91 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 1460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 186 0.068 - 0.135: 100 0.135 - 0.203: 46 0.203 - 0.270: 20 0.270 - 0.338: 44 Chirality restraints: 396 Sorted by residual: chirality pdb=" CA ASN H 103 " pdb=" N ASN H 103 " pdb=" C ASN H 103 " pdb=" CB ASN H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ASN G 103 " pdb=" N ASN G 103 " pdb=" C ASN G 103 " pdb=" CB ASN G 103 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ASN A 103 " pdb=" N ASN A 103 " pdb=" C ASN A 103 " pdb=" CB ASN A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 393 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 99 " -0.020 2.00e-02 2.50e+03 1.76e-02 5.40e+00 pdb=" CG PHE E 99 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE E 99 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 99 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 99 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 99 " 0.020 2.00e-02 2.50e+03 1.75e-02 5.37e+00 pdb=" CG PHE D 99 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE D 99 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 99 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 99 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 99 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 99 " -0.020 2.00e-02 2.50e+03 1.75e-02 5.35e+00 pdb=" CG PHE C 99 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 99 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 99 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 99 " -0.003 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 903 2.80 - 3.33: 2451 3.33 - 3.85: 4656 3.85 - 4.38: 5350 4.38 - 4.90: 9886 Nonbonded interactions: 23246 Sorted by model distance: nonbonded pdb=" O SER K 101 " pdb=" OG SER K 101 " model vdw 2.280 2.440 nonbonded pdb=" O SER D 101 " pdb=" OG SER D 101 " model vdw 2.280 2.440 nonbonded pdb=" O SER H 101 " pdb=" OG SER H 101 " model vdw 2.281 2.440 nonbonded pdb=" O SER F 101 " pdb=" OG SER F 101 " model vdw 2.281 2.440 nonbonded pdb=" O SER B 101 " pdb=" OG SER B 101 " model vdw 2.281 2.440 ... (remaining 23241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.000 Extract box with map and model: 3.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.020 0.136 2673 Z= 1.490 Angle : 2.209 15.939 3608 Z= 1.304 Chirality : 0.136 0.338 396 Planarity : 0.009 0.019 484 Dihedral : 14.467 41.919 847 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.13 % Favored : 83.87 % Rotamer: Outliers : 8.00 % Allowed : 12.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.23 % 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: -4.98 (0.33), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.297 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 143 average time/residue: 0.1119 time to fit residues: 19.4651 Evaluate side-chains 98 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0294 time to fit residues: 0.9063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2673 Z= 0.334 Angle : 0.922 5.466 3608 Z= 0.519 Chirality : 0.050 0.192 396 Planarity : 0.003 0.016 484 Dihedral : 8.655 25.942 352 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 17.45 % Allowed : 14.55 % Favored : 68.00 % 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: -4.82 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.25), residues: 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 0.312 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 146 average time/residue: 0.0786 time to fit residues: 15.0894 Evaluate side-chains 110 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0302 time to fit residues: 1.6101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2673 Z= 0.318 Angle : 0.845 5.269 3608 Z= 0.477 Chirality : 0.049 0.177 396 Planarity : 0.003 0.014 484 Dihedral : 7.119 15.940 352 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.48 % Favored : 81.52 % Rotamer: Outliers : 7.27 % Allowed : 24.00 % Favored : 68.73 % 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: -4.85 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.24), residues: 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.312 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 119 average time/residue: 0.0751 time to fit residues: 11.9631 Evaluate side-chains 102 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0417 time to fit residues: 1.4410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 chunk 30 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2673 Z= 0.358 Angle : 0.834 5.874 3608 Z= 0.469 Chirality : 0.048 0.168 396 Planarity : 0.003 0.015 484 Dihedral : 7.174 16.107 352 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 6.91 % Allowed : 26.55 % Favored : 66.55 % 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: -4.82 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.24), residues: 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.268 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 101 average time/residue: 0.0694 time to fit residues: 9.6956 Evaluate side-chains 107 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.225 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0270 time to fit residues: 1.0060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2673 Z= 0.281 Angle : 0.780 5.794 3608 Z= 0.432 Chirality : 0.045 0.165 396 Planarity : 0.003 0.017 484 Dihedral : 6.688 15.646 352 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.77 % Favored : 81.23 % Rotamer: Outliers : 5.45 % Allowed : 30.18 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.310 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.0728 time to fit residues: 11.4306 Evaluate side-chains 101 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0357 time to fit residues: 0.9044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2673 Z= 0.322 Angle : 0.796 6.448 3608 Z= 0.437 Chirality : 0.046 0.159 396 Planarity : 0.003 0.017 484 Dihedral : 6.645 15.836 352 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 7.27 % Allowed : 29.82 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.24), residues: 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.289 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 0.0695 time to fit residues: 10.4581 Evaluate side-chains 106 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0354 time to fit residues: 1.0365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.0070 overall best weight: 1.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2673 Z= 0.214 Angle : 0.765 6.456 3608 Z= 0.412 Chirality : 0.043 0.137 396 Planarity : 0.003 0.019 484 Dihedral : 6.029 15.099 352 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.77 % Favored : 81.23 % Rotamer: Outliers : 4.73 % Allowed : 33.09 % Favored : 62.18 % 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: -4.84 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.24), residues: 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.287 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 117 average time/residue: 0.0686 time to fit residues: 10.9568 Evaluate side-chains 105 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0328 time to fit residues: 0.9993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN E 104 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 104 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2673 Z= 0.234 Angle : 0.772 7.089 3608 Z= 0.413 Chirality : 0.045 0.169 396 Planarity : 0.003 0.017 484 Dihedral : 6.026 14.901 352 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.65 % Favored : 80.35 % Rotamer: Outliers : 3.64 % Allowed : 30.55 % Favored : 65.82 % 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: -4.80 (0.33), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.25), residues: 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.287 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 115 average time/residue: 0.0705 time to fit residues: 11.1897 Evaluate side-chains 109 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0402 time to fit residues: 0.8651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 0.0870 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2673 Z= 0.207 Angle : 0.772 7.250 3608 Z= 0.408 Chirality : 0.044 0.156 396 Planarity : 0.003 0.018 484 Dihedral : 5.781 14.332 352 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.06 % Favored : 80.94 % Rotamer: Outliers : 2.55 % Allowed : 32.73 % Favored : 64.73 % 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: -4.84 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.25), residues: 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.281 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 114 average time/residue: 0.0651 time to fit residues: 10.1826 Evaluate side-chains 106 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0360 time to fit residues: 0.7864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2673 Z= 0.446 Angle : 0.850 6.441 3608 Z= 0.472 Chirality : 0.051 0.174 396 Planarity : 0.004 0.013 484 Dihedral : 7.049 19.219 352 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.82 % Favored : 79.18 % Rotamer: Outliers : 3.64 % Allowed : 31.64 % Favored : 64.73 % 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: -4.98 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.23), residues: 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.301 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 107 average time/residue: 0.0651 time to fit residues: 9.6439 Evaluate side-chains 103 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0337 time to fit residues: 0.8626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.194826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.175998 restraints weight = 3851.282| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.29 r_work: 0.4246 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2673 Z= 0.220 Angle : 0.804 7.005 3608 Z= 0.425 Chirality : 0.046 0.175 396 Planarity : 0.003 0.019 484 Dihedral : 6.146 14.815 352 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.06 % Favored : 80.94 % Rotamer: Outliers : 1.09 % Allowed : 35.64 % Favored : 63.27 % 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: -4.92 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.24), residues: 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1047.89 seconds wall clock time: 19 minutes 27.42 seconds (1167.42 seconds total)