Starting phenix.real_space_refine (version: dev) on Wed Feb 22 21:38:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/02_2023/6qoz_4610.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/02_2023/6qoz_4610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/02_2023/6qoz_4610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/02_2023/6qoz_4610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/02_2023/6qoz_4610.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/02_2023/6qoz_4610.pdb" } resolution = 3.4 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 655 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17987 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "B" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "D" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "E" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "G" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "H" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "I" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 655 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Time building chain proxies: 9.80, per 1000 atoms: 0.54 Number of scatterers: 17987 At special positions: 0 Unit cell: (141.4, 152.6, 175, 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 125 16.00 O 3385 8.00 N 3011 7.00 C 11466 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: 6.62 Conformation dependent library (CDL) restraints added in 2.6 seconds 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4288 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 13.0% 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 54 through 62 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN B 52 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 103 through 109 removed outlier: 4.584A pdb=" N SER B 109 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.500A pdb=" N SER B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN E 52 " --> pdb=" O ASP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 103 through 109 removed outlier: 4.586A pdb=" N SER E 109 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'G' and resid 4 through 8 Processing helix chain 'G' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN G 52 " --> pdb=" O ASP G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 65 Processing helix chain 'G' and resid 103 through 109 removed outlier: 4.586A pdb=" N SER G 109 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 230 through 237 removed outlier: 3.500A pdb=" N SER G 237 " --> pdb=" O ASN G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 300 through 304 Processing helix chain 'H' and resid 54 through 62 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.513A pdb=" N ASN I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 Processing helix chain 'I' and resid 103 through 109 removed outlier: 4.585A pdb=" N SER I 109 " --> pdb=" O TYR I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 277 through 281 Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'C' and resid 33 through 53 135 hydrogen bonds defined for protein. 273 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: 3.68 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4973 1.33 - 1.46: 4187 1.46 - 1.58: 9102 1.58 - 1.70: 0 1.70 - 1.83: 194 Bond restraints: 18456 Sorted by residual: bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.531 -0.080 1.60e-02 3.91e+03 2.53e+01 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" N GLY D 1 " pdb=" CA GLY D 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" N GLY F 1 " pdb=" CA GLY F 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" CA PRO D 187 " pdb=" C PRO D 187 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.81e+01 ... (remaining 18451 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.13: 432 104.13 - 111.60: 7425 111.60 - 119.07: 7259 119.07 - 126.55: 9676 126.55 - 134.02: 349 Bond angle restraints: 25141 Sorted by residual: angle pdb=" N ARG I 367 " pdb=" CA ARG I 367 " pdb=" C ARG I 367 " ideal model delta sigma weight residual 110.55 118.98 -8.43 1.35e+00 5.49e-01 3.90e+01 angle pdb=" N ARG E 367 " pdb=" CA ARG E 367 " pdb=" C ARG E 367 " ideal model delta sigma weight residual 110.55 118.98 -8.43 1.35e+00 5.49e-01 3.90e+01 angle pdb=" N ARG G 367 " pdb=" CA ARG G 367 " pdb=" C ARG G 367 " ideal model delta sigma weight residual 110.55 118.94 -8.39 1.35e+00 5.49e-01 3.87e+01 angle pdb=" N ARG B 367 " pdb=" CA ARG B 367 " pdb=" C ARG B 367 " ideal model delta sigma weight residual 110.55 118.93 -8.38 1.35e+00 5.49e-01 3.85e+01 angle pdb=" N GLY C 71 " pdb=" CA GLY C 71 " pdb=" C GLY C 71 " ideal model delta sigma weight residual 112.52 104.58 7.94 1.37e+00 5.33e-01 3.36e+01 ... (remaining 25136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9750 17.68 - 35.36: 846 35.36 - 53.04: 186 53.04 - 70.72: 69 70.72 - 88.40: 20 Dihedral angle restraints: 10871 sinusoidal: 4222 harmonic: 6649 Sorted by residual: dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N ASP D 9 " pdb=" CA ASP D 9 " ideal model delta harmonic sigma weight residual 180.00 -153.20 -26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER A 8 " pdb=" C SER A 8 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " ideal model delta harmonic sigma weight residual 180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER H 8 " pdb=" C SER H 8 " pdb=" N ASP H 9 " pdb=" CA ASP H 9 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 10868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2338 0.121 - 0.242: 424 0.242 - 0.362: 22 0.362 - 0.483: 4 0.483 - 0.604: 4 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" CA ASN I 174 " pdb=" N ASN I 174 " pdb=" C ASN I 174 " pdb=" CB ASN I 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" CA ASN G 174 " pdb=" N ASN G 174 " pdb=" C ASN G 174 " pdb=" CB ASN G 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 ... (remaining 2789 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 255 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO G 256 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 256 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 255 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO I 256 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 255 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO E 256 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 256 " 0.029 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 23 1.97 - 2.71: 591 2.71 - 3.44: 24257 3.44 - 4.17: 46687 4.17 - 4.90: 80930 Nonbonded interactions: 152488 Sorted by model distance: nonbonded pdb=" CA GLY B 53 " pdb=" CD2 LEU C 35 " model vdw 1.243 3.860 nonbonded pdb=" O GLY B 53 " pdb=" CD1 LEU C 35 " model vdw 1.334 3.460 nonbonded pdb=" O GLY G 53 " pdb=" CD GLU C 32 " model vdw 1.352 3.270 nonbonded pdb=" OD2 ASP G 49 " pdb=" CG1 VAL C 68 " model vdw 1.422 3.460 nonbonded pdb=" N GLN G 54 " pdb=" N GLU C 32 " model vdw 1.450 3.200 ... (remaining 152483 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 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' } 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 125 5.16 5 C 11466 2.51 5 N 3011 2.21 5 O 3385 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 14.490 Check model and map are aligned: 0.260 Process input model: 42.880 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 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 : 0.011 0.080 18456 Z= 0.746 Angle : 1.457 10.725 25141 Z= 0.897 Chirality : 0.092 0.604 2792 Planarity : 0.006 0.055 3245 Dihedral : 15.400 88.397 6583 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.03 % Favored : 93.05 % Rotamer Outliers : 5.13 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -3.28 (0.15), residues: 2289 helix: -2.98 (0.27), residues: 224 sheet: -2.11 (0.16), residues: 829 loop : -2.02 (0.16), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 526 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 7 residues processed: 591 average time/residue: 0.3322 time to fit residues: 286.5281 Evaluate side-chains 282 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2103 time to fit residues: 5.3378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 71 HIS A 112 GLN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN E 27 GLN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN F 48 ASN F 112 GLN F 128 ASN F 158 GLN G 27 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 130 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 48 ASN H 158 GLN I 27 GLN I 52 ASN I 233 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 18456 Z= 0.196 Angle : 0.647 11.058 25141 Z= 0.330 Chirality : 0.046 0.193 2792 Planarity : 0.005 0.047 3245 Dihedral : 5.622 22.098 2459 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.62 % Favored : 97.16 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -2.24 (0.16), residues: 2289 helix: -1.74 (0.32), residues: 228 sheet: -1.39 (0.18), residues: 756 loop : -1.45 (0.16), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 322 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 33 residues processed: 378 average time/residue: 0.2629 time to fit residues: 161.1254 Evaluate side-chains 272 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 2.135 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1643 time to fit residues: 13.4033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS B 4 ASN B 233 ASN D 141 GLN E 4 ASN E 27 GLN E 233 ASN E 331 HIS F 73 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN G 233 ASN G 331 HIS I 4 ASN ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.9273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.134 18456 Z= 0.502 Angle : 0.902 13.996 25141 Z= 0.465 Chirality : 0.054 0.196 2792 Planarity : 0.006 0.052 3245 Dihedral : 5.972 25.255 2459 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.07 % Favored : 93.75 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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 (0.16), residues: 2289 helix: -1.72 (0.36), residues: 180 sheet: -0.90 (0.19), residues: 768 loop : -2.09 (0.14), residues: 1341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 236 time to evaluate : 2.173 Fit side-chains outliers start: 91 outliers final: 38 residues processed: 309 average time/residue: 0.2605 time to fit residues: 129.0312 Evaluate side-chains 218 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1637 time to fit residues: 14.6077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 58 optimal weight: 0.1980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 93 ASN E 27 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN H 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.9504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 18456 Z= 0.186 Angle : 0.563 8.859 25141 Z= 0.279 Chirality : 0.045 0.151 2792 Planarity : 0.005 0.051 3245 Dihedral : 4.757 18.656 2459 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.01 % Favored : 96.81 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -1.86 (0.17), residues: 2289 helix: -0.91 (0.41), residues: 180 sheet: -0.56 (0.20), residues: 768 loop : -1.73 (0.15), residues: 1341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 2.155 Fit side-chains outliers start: 47 outliers final: 28 residues processed: 223 average time/residue: 0.3013 time to fit residues: 107.9569 Evaluate side-chains 189 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1692 time to fit residues: 12.0733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 54 optimal weight: 40.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 331 HIS F 99 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 1.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 18456 Z= 0.353 Angle : 0.657 12.615 25141 Z= 0.323 Chirality : 0.048 0.163 2792 Planarity : 0.005 0.051 3245 Dihedral : 4.793 19.881 2459 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.15 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -2.05 (0.17), residues: 2289 helix: -1.71 (0.32), residues: 228 sheet: -0.80 (0.18), residues: 878 loop : -1.70 (0.16), residues: 1183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 2.062 Fit side-chains outliers start: 54 outliers final: 16 residues processed: 218 average time/residue: 0.2967 time to fit residues: 100.9992 Evaluate side-chains 174 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1652 time to fit residues: 7.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 1.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 18456 Z= 0.271 Angle : 0.581 11.786 25141 Z= 0.283 Chirality : 0.045 0.158 2792 Planarity : 0.004 0.052 3245 Dihedral : 4.563 18.561 2459 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -1.91 (0.17), residues: 2289 helix: -1.59 (0.33), residues: 228 sheet: -0.59 (0.19), residues: 850 loop : -1.70 (0.16), residues: 1211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 2.306 Fit side-chains outliers start: 36 outliers final: 13 residues processed: 194 average time/residue: 0.2993 time to fit residues: 89.9764 Evaluate side-chains 169 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1697 time to fit residues: 7.1951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 1.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 18456 Z= 0.237 Angle : 0.564 12.969 25141 Z= 0.267 Chirality : 0.044 0.153 2792 Planarity : 0.004 0.052 3245 Dihedral : 4.368 17.620 2459 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -1.63 (0.17), residues: 2289 helix: -1.43 (0.34), residues: 224 sheet: -0.46 (0.20), residues: 812 loop : -1.43 (0.16), residues: 1253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 2.190 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 182 average time/residue: 0.3163 time to fit residues: 88.1925 Evaluate side-chains 167 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1683 time to fit residues: 5.5923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 1.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 18456 Z= 0.354 Angle : 0.633 14.484 25141 Z= 0.303 Chirality : 0.046 0.154 2792 Planarity : 0.004 0.052 3245 Dihedral : 4.610 18.550 2459 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -1.59 (0.17), residues: 2289 helix: -1.48 (0.34), residues: 220 sheet: -0.04 (0.21), residues: 740 loop : -1.62 (0.15), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 2.133 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 184 average time/residue: 0.2947 time to fit residues: 84.3925 Evaluate side-chains 170 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1731 time to fit residues: 7.4465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 1.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 18456 Z= 0.257 Angle : 0.580 13.622 25141 Z= 0.273 Chirality : 0.044 0.153 2792 Planarity : 0.004 0.053 3245 Dihedral : 4.442 17.790 2459 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -1.55 (0.17), residues: 2289 helix: -1.54 (0.34), residues: 228 sheet: -0.05 (0.21), residues: 706 loop : -1.51 (0.15), residues: 1355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 2.310 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 171 average time/residue: 0.3057 time to fit residues: 81.4192 Evaluate side-chains 160 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1597 time to fit residues: 3.9671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 147 optimal weight: 0.4980 chunk 222 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.097 18456 Z= 0.459 Angle : 0.693 15.090 25141 Z= 0.335 Chirality : 0.048 0.166 2792 Planarity : 0.005 0.053 3245 Dihedral : 4.886 19.026 2459 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -1.89 (0.17), residues: 2289 helix: -1.83 (0.32), residues: 224 sheet: -0.13 (0.21), residues: 748 loop : -1.89 (0.15), residues: 1317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 2.073 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 174 average time/residue: 0.3217 time to fit residues: 85.9306 Evaluate side-chains 163 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1920 time to fit residues: 4.0894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 5.9990 chunk 54 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075239 restraints weight = 37495.955| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.19 r_work: 0.2995 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 1.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 18456 Z= 0.198 Angle : 0.567 13.149 25141 Z= 0.267 Chirality : 0.044 0.158 2792 Planarity : 0.004 0.054 3245 Dihedral : 4.482 20.143 2459 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -1.71 (0.17), residues: 2289 helix: -1.61 (0.33), residues: 228 sheet: -0.05 (0.21), residues: 742 loop : -1.74 (0.15), residues: 1319 =============================================================================== Job complete usr+sys time: 3668.99 seconds wall clock time: 67 minutes 23.77 seconds (4043.77 seconds total)