Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:30:03 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/12_2021/7cz6_30507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/12_2021/7cz6_30507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/12_2021/7cz6_30507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/12_2021/7cz6_30507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/12_2021/7cz6_30507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/12_2021/7cz6_30507.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5442 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 116, 'PCIS': 1} Chain: "C" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 116, 'PCIS': 1} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 116, 'PCIS': 1} Chain: "D" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 116, 'PCIS': 1} Chain: "E" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 116, 'PCIS': 1} Chain: "F" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 116, 'PCIS': 1} Time building chain proxies: 3.49, per 1000 atoms: 0.64 Number of scatterers: 5442 At special positions: 0 Unit cell: (73.03, 71.94, 338.99, 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 24 16.00 O 1098 8.00 N 840 7.00 C 3480 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 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 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 919.3 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id= 1, first strand: chain 'C' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR C 275 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 318 " --> pdb=" O TYR C 275 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 262 through 264 Processing sheet with id= 3, first strand: chain 'A' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR A 275 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 318 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 262 through 264 Processing sheet with id= 5, first strand: chain 'B' and resid 248 through 254 removed outlier: 5.248A pdb=" N TYR B 275 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 318 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 262 through 264 Processing sheet with id= 7, first strand: chain 'D' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR D 275 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 318 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 262 through 264 Processing sheet with id= 9, first strand: chain 'E' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR E 275 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 318 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 262 through 264 Processing sheet with id= 11, first strand: chain 'F' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR F 275 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR F 318 " --> pdb=" O TYR F 275 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 262 through 264 180 hydrogen bonds defined for protein. 486 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: 1.30 Time building geometry restraints manager: 2.66 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: 1635 1.34 - 1.46: 1155 1.46 - 1.58: 2742 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5568 Sorted by residual: bond pdb=" CA PRO F 269 " pdb=" C PRO F 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.45e+00 bond pdb=" CA PRO D 269 " pdb=" C PRO D 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.43e+00 bond pdb=" CA PRO C 269 " pdb=" C PRO C 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.38e+00 bond pdb=" CA PRO E 269 " pdb=" C PRO E 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 bond pdb=" CA PRO B 269 " pdb=" C PRO B 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 294 106.95 - 113.72: 3176 113.72 - 120.49: 1917 120.49 - 127.26: 2245 127.26 - 134.03: 48 Bond angle restraints: 7680 Sorted by residual: angle pdb=" N TYR E 304 " pdb=" CA TYR E 304 " pdb=" C TYR E 304 " ideal model delta sigma weight residual 107.60 121.35 -13.75 1.83e+00 2.99e-01 5.65e+01 angle pdb=" N TYR D 304 " pdb=" CA TYR D 304 " pdb=" C TYR D 304 " ideal model delta sigma weight residual 107.60 121.34 -13.74 1.83e+00 2.99e-01 5.64e+01 angle pdb=" N TYR C 304 " pdb=" CA TYR C 304 " pdb=" C TYR C 304 " ideal model delta sigma weight residual 107.60 121.32 -13.72 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 107.60 121.32 -13.72 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR B 304 " pdb=" CA TYR B 304 " pdb=" C TYR B 304 " ideal model delta sigma weight residual 107.60 121.31 -13.71 1.83e+00 2.99e-01 5.62e+01 ... (remaining 7675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 3032 11.98 - 23.97: 148 23.97 - 35.95: 12 35.95 - 47.94: 18 47.94 - 59.92: 6 Dihedral angle restraints: 3216 sinusoidal: 1080 harmonic: 2136 Sorted by residual: dihedral pdb=" CA GLY E 317 " pdb=" C GLY E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY A 317 " pdb=" C GLY A 317 " pdb=" N THR A 318 " pdb=" CA THR A 318 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY D 317 " pdb=" C GLY D 317 " pdb=" N THR D 318 " pdb=" CA THR D 318 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 3213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 841 0.061 - 0.122: 130 0.122 - 0.182: 13 0.182 - 0.243: 0 0.243 - 0.304: 6 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA TYR F 304 " pdb=" N TYR F 304 " pdb=" C TYR F 304 " pdb=" CB TYR F 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA TYR E 304 " pdb=" N TYR E 304 " pdb=" C TYR E 304 " pdb=" CB TYR E 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA TYR C 304 " pdb=" N TYR C 304 " pdb=" C TYR C 304 " pdb=" CB TYR C 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 987 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 260 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO D 261 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 268 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO E 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 269 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 268 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO C 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.033 5.00e-02 4.00e+02 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 15 1.82 - 2.59: 144 2.59 - 3.36: 7616 3.36 - 4.13: 12029 4.13 - 4.90: 21043 Nonbonded interactions: 40847 Sorted by model distance: nonbonded pdb=" O ASP B 309 " pdb=" OD2 ASP D 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP D 309 " pdb=" OD2 ASP E 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP C 309 " pdb=" OD2 ASP B 309 " model vdw 1.048 3.040 nonbonded pdb=" OD2 ASP C 309 " pdb=" O ASP F 309 " model vdw 1.048 3.040 nonbonded pdb=" O ASP E 309 " pdb=" OD2 ASP F 309 " model vdw 1.048 3.040 ... (remaining 40842 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' } 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 24 5.16 5 C 3480 2.51 5 N 840 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.830 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 18.500 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:1.900 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 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 : 0.009 0.041 5568 Z= 0.577 Angle : 1.616 13.750 7680 Z= 1.064 Chirality : 0.052 0.304 990 Planarity : 0.008 0.062 954 Dihedral : 8.571 59.920 1848 Min Nonbonded Distance : 1.047 Molprobity Statistics. All-atom Clashscore : 53.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.30), residues: 744 helix: None (None), residues: 0 sheet: -0.79 (0.34), residues: 216 loop : -1.29 (0.27), residues: 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 0.668 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 outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1296 time to fit residues: 42.1107 Evaluate side-chains 169 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN C 360 GLN B 282 GLN B 305 GLN B 360 GLN D 276 GLN D 282 GLN D 305 GLN D 360 GLN E 305 GLN E 360 GLN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5568 Z= 0.253 Angle : 0.772 8.533 7680 Z= 0.421 Chirality : 0.051 0.167 990 Planarity : 0.006 0.056 954 Dihedral : 7.528 24.442 768 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.25 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -1.20 (0.27), residues: 366 loop : -1.74 (0.28), residues: 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 233 average time/residue: 0.1315 time to fit residues: 41.2492 Evaluate side-chains 195 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0492 time to fit residues: 0.7813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.0970 chunk 20 optimal weight: 0.0370 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN C 305 GLN B 276 GLN B 282 GLN D 282 GLN E 282 GLN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 5568 Z= 0.245 Angle : 0.709 7.116 7680 Z= 0.385 Chirality : 0.050 0.192 990 Planarity : 0.006 0.061 954 Dihedral : 6.835 20.931 768 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.33 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -1.21 (0.27), residues: 360 loop : -1.84 (0.29), residues: 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1294 time to fit residues: 38.3055 Evaluate side-chains 189 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 20.0000 chunk 49 optimal weight: 0.0040 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 50.0000 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 0.0770 chunk 69 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN B 282 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN F 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5568 Z= 0.229 Angle : 0.665 7.318 7680 Z= 0.356 Chirality : 0.048 0.182 990 Planarity : 0.006 0.068 954 Dihedral : 6.525 21.059 768 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.28 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -1.22 (0.27), residues: 372 loop : -1.75 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1222 time to fit residues: 37.6821 Evaluate side-chains 200 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 40.0000 chunk 17 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN B 305 GLN D 282 GLN F 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 5568 Z= 0.402 Angle : 0.712 6.293 7680 Z= 0.391 Chirality : 0.049 0.161 990 Planarity : 0.007 0.072 954 Dihedral : 6.671 21.237 768 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.34 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -1.13 (0.26), residues: 372 loop : -1.96 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.684 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1250 time to fit residues: 37.8491 Evaluate side-chains 193 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN B 256 ASN B 282 GLN D 253 ASN E 253 ASN F 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 5568 Z= 0.408 Angle : 0.716 5.977 7680 Z= 0.394 Chirality : 0.049 0.175 990 Planarity : 0.007 0.071 954 Dihedral : 6.632 22.188 768 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.36 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -1.06 (0.26), residues: 372 loop : -2.09 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 0.649 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.1302 time to fit residues: 37.4138 Evaluate side-chains 180 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0540 time to fit residues: 0.9136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 50.0000 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 5568 Z= 0.343 Angle : 0.715 7.166 7680 Z= 0.381 Chirality : 0.049 0.172 990 Planarity : 0.007 0.069 954 Dihedral : 6.552 21.826 768 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.33 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -1.02 (0.26), residues: 372 loop : -2.10 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1311 time to fit residues: 37.3095 Evaluate side-chains 182 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN C 282 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 5568 Z= 0.319 Angle : 0.701 6.984 7680 Z= 0.372 Chirality : 0.050 0.173 990 Planarity : 0.006 0.069 954 Dihedral : 6.603 22.465 768 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.22 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -0.94 (0.25), residues: 372 loop : -2.02 (0.30), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1355 time to fit residues: 35.3450 Evaluate side-chains 178 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 9.9990 chunk 38 optimal weight: 0.0270 chunk 28 optimal weight: 20.0000 chunk 50 optimal weight: 0.0370 chunk 19 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN B 256 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5568 Z= 0.176 Angle : 0.677 9.463 7680 Z= 0.352 Chirality : 0.051 0.175 990 Planarity : 0.006 0.070 954 Dihedral : 6.085 20.486 768 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -0.62 (0.30), residues: 306 loop : -1.87 (0.27), residues: 438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1257 time to fit residues: 39.1519 Evaluate side-chains 196 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 5568 Z= 0.386 Angle : 0.724 7.143 7680 Z= 0.386 Chirality : 0.051 0.200 990 Planarity : 0.006 0.070 954 Dihedral : 6.421 24.311 768 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.02 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -0.64 (0.29), residues: 306 loop : -1.92 (0.27), residues: 438 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.630 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1323 time to fit residues: 34.5982 Evaluate side-chains 180 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 50.0000 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 50.0000 chunk 10 optimal weight: 50.0000 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.203752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138429 restraints weight = 12163.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142429 restraints weight = 6853.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144946 restraints weight = 4737.323| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 5568 Z= 0.268 Angle : 0.693 8.229 7680 Z= 0.364 Chirality : 0.050 0.181 990 Planarity : 0.006 0.065 954 Dihedral : 6.332 22.511 768 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.29), residues: 744 helix: None (None), residues: 0 sheet: -0.61 (0.29), residues: 306 loop : -1.91 (0.27), residues: 438 =============================================================================== Job complete usr+sys time: 1428.31 seconds wall clock time: 26 minutes 36.68 seconds (1596.68 seconds total)