Starting phenix.real_space_refine (version: dev) on Sat Feb 18 10:49:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/02_2023/6xss_22305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/02_2023/6xss_22305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/02_2023/6xss_22305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/02_2023/6xss_22305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/02_2023/6xss_22305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/02_2023/6xss_22305.pdb" } resolution = 3.7 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= -0.001 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "A ASP 129": "OD1" <-> "OD2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "B" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "D" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Time building chain proxies: 4.87, per 1000 atoms: 0.61 Number of scatterers: 8048 At special positions: 0 Unit cell: (121.119, 121.119, 77.31, 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 8 16.00 O 1620 8.00 N 1464 7.00 C 4956 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: 3.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 95.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.811A pdb=" N VAL A 5 " --> pdb=" O ALA A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 65 Processing helix chain 'A' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG A 72 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 Processing helix chain 'A' and resid 127 through 155 Processing helix chain 'A' and resid 156 through 180 Processing helix chain 'A' and resid 183 through 211 Processing helix chain 'A' and resid 212 through 236 Processing helix chain 'A' and resid 239 through 260 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 Processing helix chain 'B' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG B 72 " --> pdb=" O MET B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 Processing helix chain 'B' and resid 127 through 155 Processing helix chain 'B' and resid 156 through 180 Processing helix chain 'B' and resid 183 through 211 Processing helix chain 'B' and resid 212 through 236 Processing helix chain 'B' and resid 239 through 260 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 65 Processing helix chain 'C' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 124 Processing helix chain 'C' and resid 127 through 155 Processing helix chain 'C' and resid 156 through 180 Processing helix chain 'C' and resid 183 through 211 Processing helix chain 'C' and resid 212 through 236 Processing helix chain 'C' and resid 239 through 260 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 127 through 155 Processing helix chain 'D' and resid 156 through 180 Processing helix chain 'D' and resid 183 through 211 Processing helix chain 'D' and resid 212 through 236 Processing helix chain 'D' and resid 239 through 260 804 hydrogen bonds defined for protein. 2412 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: 2.61 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2960 1.34 - 1.46: 365 1.46 - 1.57: 4755 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 8096 Sorted by residual: bond pdb=" N ASN A 15 " pdb=" CA ASN A 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.92e-01 bond pdb=" N ASN B 15 " pdb=" CA ASN B 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.81e-01 bond pdb=" N ASN C 15 " pdb=" CA ASN C 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.63e-01 bond pdb=" N ASN D 15 " pdb=" CA ASN D 15 " ideal model delta sigma weight residual 1.459 1.471 -0.013 1.32e-02 5.74e+03 9.34e-01 bond pdb=" C GLY D 49 " pdb=" O GLY D 49 " ideal model delta sigma weight residual 1.240 1.229 0.012 1.29e-02 6.01e+03 7.97e-01 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 150 107.17 - 113.86: 4703 113.86 - 120.56: 3613 120.56 - 127.25: 2414 127.25 - 133.95: 52 Bond angle restraints: 10932 Sorted by residual: angle pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sigma weight residual 116.30 129.90 -13.60 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU D 222 " pdb=" CB LEU D 222 " pdb=" CG LEU D 222 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU C 222 " pdb=" CB LEU C 222 " pdb=" CG LEU C 222 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU B 222 " pdb=" CB LEU B 222 " pdb=" CG LEU B 222 " ideal model delta sigma weight residual 116.30 129.84 -13.54 3.50e+00 8.16e-02 1.50e+01 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 114.85 110.60 4.25 1.35e+00 5.49e-01 9.90e+00 ... (remaining 10927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4804 17.34 - 34.68: 360 34.68 - 52.02: 40 52.02 - 69.37: 4 69.37 - 86.71: 12 Dihedral angle restraints: 5220 sinusoidal: 2156 harmonic: 3064 Sorted by residual: dihedral pdb=" N ASN C 15 " pdb=" C ASN C 15 " pdb=" CA ASN C 15 " pdb=" CB ASN C 15 " ideal model delta harmonic sigma weight residual 122.80 132.00 -9.20 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N ASN A 15 " pdb=" C ASN A 15 " pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " ideal model delta harmonic sigma weight residual 122.80 131.99 -9.19 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N ASN B 15 " pdb=" C ASN B 15 " pdb=" CA ASN B 15 " pdb=" CB ASN B 15 " ideal model delta harmonic sigma weight residual 122.80 131.96 -9.16 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1198 0.066 - 0.131: 94 0.131 - 0.197: 4 0.197 - 0.263: 0 0.263 - 0.328: 4 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ASN C 15 " pdb=" N ASN C 15 " pdb=" C ASN C 15 " pdb=" CB ASN C 15 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASN A 15 " pdb=" N ASN A 15 " pdb=" C ASN A 15 " pdb=" CB ASN A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASN B 15 " pdb=" N ASN B 15 " pdb=" C ASN B 15 " pdb=" CB ASN B 15 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1297 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 14 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C LEU D 14 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU D 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN D 15 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 14 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LEU C 14 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU C 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN C 15 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 14 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C LEU A 14 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 15 " 0.008 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 49 2.45 - 3.07: 5477 3.07 - 3.68: 12994 3.68 - 4.29: 17762 4.29 - 4.90: 28573 Nonbonded interactions: 64855 Sorted by model distance: nonbonded pdb=" CB ALA D 94 " pdb=" CD2 LEU D 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA A 94 " pdb=" CD2 LEU A 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA C 94 " pdb=" CD2 LEU C 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA B 94 " pdb=" CD2 LEU B 148 " model vdw 1.844 3.880 nonbonded pdb=" NH2 ARG A 83 " pdb=" OE1 GLU A 142 " model vdw 1.982 2.520 ... (remaining 64850 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' } 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 8 5.16 5 C 4956 2.51 5 N 1464 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.270 Check model and map are aligned: 0.120 Process input model: 24.890 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 8096 Z= 0.176 Angle : 0.628 13.605 10932 Z= 0.356 Chirality : 0.038 0.328 1300 Planarity : 0.003 0.024 1468 Dihedral : 12.310 86.708 3196 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1032 helix: 0.08 (0.14), residues: 976 sheet: None (None), residues: 0 loop : -3.14 (1.01), residues: 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 0.884 Fit side-chains 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: 307 average time/residue: 0.3237 time to fit residues: 119.7524 Evaluate side-chains 144 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 131 ASN C 15 ASN C 131 ASN C 234 GLN D 15 ASN D 131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8096 Z= 0.246 Angle : 0.705 11.156 10932 Z= 0.340 Chirality : 0.038 0.149 1300 Planarity : 0.004 0.042 1468 Dihedral : 3.428 11.907 1148 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 1.70 % 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: 1.19 (0.24), residues: 1032 helix: 1.06 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -3.96 (1.01), residues: 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.005 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 outliers start: 14 outliers final: 7 residues processed: 169 average time/residue: 0.2401 time to fit residues: 53.3882 Evaluate side-chains 131 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0747 time to fit residues: 2.3057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 0.0070 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8096 Z= 0.181 Angle : 0.645 10.490 10932 Z= 0.308 Chirality : 0.035 0.137 1300 Planarity : 0.004 0.045 1468 Dihedral : 3.406 11.905 1148 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 2.18 % 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: 2.18 (0.24), residues: 1032 helix: 1.70 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -3.49 (0.85), residues: 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 162 average time/residue: 0.2022 time to fit residues: 44.6841 Evaluate side-chains 124 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0827 time to fit residues: 2.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN D 92 GLN D 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8096 Z= 0.270 Angle : 0.685 10.859 10932 Z= 0.329 Chirality : 0.037 0.164 1300 Planarity : 0.005 0.046 1468 Dihedral : 3.405 11.985 1148 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.24), residues: 1032 helix: 1.89 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -4.28 (0.71), residues: 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 129 average time/residue: 0.2377 time to fit residues: 41.0644 Evaluate side-chains 127 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0742 time to fit residues: 3.5624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8096 Z= 0.281 Angle : 0.683 10.671 10932 Z= 0.330 Chirality : 0.037 0.149 1300 Planarity : 0.005 0.045 1468 Dihedral : 3.452 11.794 1148 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.82 % 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: 2.42 (0.24), residues: 1032 helix: 1.89 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -4.58 (0.63), residues: 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 135 average time/residue: 0.2010 time to fit residues: 37.6282 Evaluate side-chains 114 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0767 time to fit residues: 2.3067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8096 Z= 0.199 Angle : 0.687 12.561 10932 Z= 0.323 Chirality : 0.036 0.138 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.447 12.134 1148 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.82 % 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: 2.72 (0.24), residues: 1032 helix: 2.06 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.41 (0.73), residues: 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 133 average time/residue: 0.2165 time to fit residues: 39.9322 Evaluate side-chains 117 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0922 time to fit residues: 2.5817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8096 Z= 0.254 Angle : 0.720 12.092 10932 Z= 0.340 Chirality : 0.038 0.189 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.485 11.688 1148 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.24), residues: 1032 helix: 2.02 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -4.57 (0.65), residues: 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.2094 time to fit residues: 35.9142 Evaluate side-chains 118 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0824 time to fit residues: 2.8518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 0.0170 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8096 Z= 0.268 Angle : 0.749 12.299 10932 Z= 0.356 Chirality : 0.039 0.214 1300 Planarity : 0.005 0.042 1468 Dihedral : 3.524 12.939 1148 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.24), residues: 1032 helix: 1.91 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.87 (0.70), residues: 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 117 average time/residue: 0.1928 time to fit residues: 31.8318 Evaluate side-chains 106 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0725 time to fit residues: 2.0147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8096 Z= 0.198 Angle : 0.747 13.192 10932 Z= 0.346 Chirality : 0.037 0.159 1300 Planarity : 0.004 0.042 1468 Dihedral : 3.549 13.086 1148 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.24), residues: 1032 helix: 2.03 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -4.13 (0.72), residues: 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 134 average time/residue: 0.2036 time to fit residues: 37.5915 Evaluate side-chains 112 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0709 time to fit residues: 1.8800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 8096 Z= 0.313 Angle : 0.830 16.013 10932 Z= 0.395 Chirality : 0.041 0.253 1300 Planarity : 0.005 0.051 1468 Dihedral : 3.600 13.819 1148 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.36 % 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: 2.34 (0.24), residues: 1032 helix: 1.83 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.95 (0.65), residues: 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.2227 time to fit residues: 33.6864 Evaluate side-chains 106 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0748 time to fit residues: 1.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 0.0000 chunk 72 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.106391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.073814 restraints weight = 27400.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076231 restraints weight = 15871.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.077678 restraints weight = 11464.332| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 8096 Z= 0.221 Angle : 0.788 15.263 10932 Z= 0.368 Chirality : 0.038 0.216 1300 Planarity : 0.004 0.041 1468 Dihedral : 3.577 14.240 1148 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.24), residues: 1032 helix: 1.88 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -4.26 (0.69), residues: 48 =============================================================================== Job complete usr+sys time: 1583.44 seconds wall clock time: 29 minutes 50.96 seconds (1790.96 seconds total)