Starting phenix.real_space_refine (version: dev) on Mon Apr 4 17:28:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/04_2022/6xss_22305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/04_2022/6xss_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_22305/04_2022/6xss_22305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/04_2022/6xss_22305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/04_2022/6xss_22305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/04_2022/6xss_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 4.88, 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: 3.57 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: 0.26 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: 2.57 Time building geometry restraints manager: 3.83 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 3.990 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.080 Process input model: 25.230 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- 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 : 1.010 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: 0.2933 time to fit residues: 109.8100 Evaluate side-chains 140 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3384 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 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: 0.7880 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 8096 Z= 0.263 Angle : 0.732 11.685 10932 Z= 0.354 Chirality : 0.038 0.151 1300 Planarity : 0.005 0.042 1468 Dihedral : 3.451 12.201 1148 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.06 % 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: 1.20 (0.24), residues: 1032 helix: 1.06 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.07 (1.02), 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 185 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.039 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: 17 outliers final: 10 residues processed: 174 average time/residue: 0.2197 time to fit residues: 50.6102 Evaluate side-chains 128 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0709 time to fit residues: 2.6845 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 8096 Z= 0.229 Angle : 0.684 10.633 10932 Z= 0.330 Chirality : 0.035 0.143 1300 Planarity : 0.004 0.045 1468 Dihedral : 3.424 11.500 1148 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 2.06 % 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: 2.06 (0.25), residues: 1032 helix: 1.60 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -3.33 (0.93), residues: 44 *********************** 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 167 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 158 average time/residue: 0.1987 time to fit residues: 42.6303 Evaluate side-chains 120 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0850 time to fit residues: 2.1901 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 8096 Z= 0.351 Angle : 0.749 10.490 10932 Z= 0.368 Chirality : 0.037 0.161 1300 Planarity : 0.005 0.045 1468 Dihedral : 3.475 12.673 1148 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.24), residues: 1032 helix: 1.68 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.17 (0.81), residues: 44 *********************** 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 155 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 138 average time/residue: 0.1946 time to fit residues: 37.0342 Evaluate side-chains 127 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0738 time to fit residues: 3.8526 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 180 ASN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.118 8096 Z= 0.289 Angle : 0.746 12.784 10932 Z= 0.357 Chirality : 0.036 0.146 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.491 11.940 1148 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 2.52 (0.24), residues: 1032 helix: 1.91 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -3.96 (0.81), residues: 44 *********************** 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 156 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 147 average time/residue: 0.1845 time to fit residues: 37.7986 Evaluate side-chains 118 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0722 time to fit residues: 1.8334 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.167 8096 Z= 0.356 Angle : 0.763 11.909 10932 Z= 0.374 Chirality : 0.036 0.132 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.459 11.876 1148 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.06 % 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: 2.71 (0.24), residues: 1032 helix: 2.05 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.27 (0.71), 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 145 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 137 average time/residue: 0.1928 time to fit residues: 36.6831 Evaluate side-chains 112 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0721 time to fit residues: 2.5950 ------------------------------------------------------------------------------- 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: 9.9990 chunk 57 optimal weight: 7.9990 chunk 73 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.260 8096 Z= 0.495 Angle : 0.856 16.524 10932 Z= 0.426 Chirality : 0.039 0.181 1300 Planarity : 0.005 0.042 1468 Dihedral : 3.515 12.256 1148 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.09 % 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: 2.53 (0.24), residues: 1032 helix: 1.92 (0.15), residues: 992 sheet: None (None), residues: 0 loop : -4.64 (0.75), residues: 40 *********************** 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 128 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 122 average time/residue: 0.1866 time to fit residues: 31.6449 Evaluate side-chains 109 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0812 time to fit residues: 2.2980 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.425 8096 Z= 0.682 Angle : 0.919 24.194 10932 Z= 0.482 Chirality : 0.037 0.208 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.504 13.033 1148 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.46 % 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: 2.63 (0.24), residues: 1032 helix: 1.99 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.23 (0.74), 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 139 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 0.1731 time to fit residues: 32.1654 Evaluate side-chains 115 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0712 time to fit residues: 2.5708 ------------------------------------------------------------------------------- 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: 6.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.474 8096 Z= 0.769 Angle : 1.368 73.899 10932 Z= 0.623 Chirality : 0.038 0.288 1300 Planarity : 0.005 0.092 1468 Dihedral : 3.601 20.446 1148 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 2.61 (0.24), residues: 1032 helix: 1.98 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.23 (0.74), residues: 44 *********************** 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 114 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.1817 time to fit residues: 29.1898 Evaluate side-chains 104 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0777 time to fit residues: 1.5040 ------------------------------------------------------------------------------- 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: 4.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 0.795 8096 Z= 1.088 Angle : 1.649 106.090 10932 Z= 0.730 Chirality : 0.040 0.485 1300 Planarity : 0.005 0.085 1468 Dihedral : 3.630 19.454 1148 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.10 % 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: 1.98 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.23 (0.74), 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 109 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 0.1818 time to fit residues: 27.4864 Evaluate side-chains 106 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0850 time to fit residues: 2.1312 ------------------------------------------------------------------------------- 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: 5.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.0070 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.106979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074885 restraints weight = 27412.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.076982 restraints weight = 16399.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078236 restraints weight = 12092.017| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 0.795 8096 Z= 1.088 Angle : 1.649 106.090 10932 Z= 0.730 Chirality : 0.040 0.485 1300 Planarity : 0.005 0.085 1468 Dihedral : 3.630 19.454 1148 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.10 % 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: 1.98 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.23 (0.74), residues: 44 =============================================================================== Job complete usr+sys time: 1501.74 seconds wall clock time: 28 minutes 6.93 seconds (1686.93 seconds total)