Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 20:55:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/07_2023/8dki_27489_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/07_2023/8dki_27489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/07_2023/8dki_27489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/07_2023/8dki_27489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/07_2023/8dki_27489_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dki_27489/07_2023/8dki_27489_neut.pdb" } resolution = 3.32 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= 0.004 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2858 2.51 5 N 703 2.21 5 O 789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 4365 Number of models: 1 Model: "" Number of chains: 3 Chain: "P" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2679 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 871 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 2.63, per 1000 atoms: 0.60 Number of scatterers: 4365 At special positions: 0 Unit cell: (78.492, 64.988, 114.784, 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 15 16.00 O 789 8.00 N 703 7.00 C 2858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 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: 1.72 Conformation dependent library (CDL) restraints added in 674.3 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 7 sheets defined 38.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'P' and resid 120 through 141 Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.618A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 180 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 Processing helix chain 'P' and resid 234 through 257 removed outlier: 3.662A pdb=" N VAL P 257 " --> pdb=" O ILE P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 279 removed outlier: 3.586A pdb=" N PHE P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE P 269 " --> pdb=" O PHE P 265 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 292 removed outlier: 3.748A pdb=" N TYR P 291 " --> pdb=" O MET P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.685A pdb=" N VAL P 302 " --> pdb=" O SER P 298 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR P 321 " --> pdb=" O PHE P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 330 Processing helix chain 'P' and resid 332 through 355 removed outlier: 3.627A pdb=" N PHE P 336 " --> pdb=" O ASP P 332 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.002A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.762A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 26 through 27 removed outlier: 3.831A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 31 through 35 removed outlier: 3.934A pdb=" N VAL P 32 " --> pdb=" O ARG P 114 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.582A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.648A pdb=" N ILE B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.426A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.351A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.88 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: 885 1.33 - 1.45: 1158 1.45 - 1.57: 2420 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4485 Sorted by residual: bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.19e+01 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.51e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.34e-02 5.57e+03 6.21e+00 bond pdb=" C PHE P 317 " pdb=" O PHE P 317 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.19e-02 7.06e+03 5.45e+00 bond pdb=" C MET P 316 " pdb=" O MET P 316 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.26e-02 6.30e+03 4.55e+00 ... (remaining 4480 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.47: 115 106.47 - 113.35: 2401 113.35 - 120.24: 1580 120.24 - 127.12: 1966 127.12 - 134.01: 55 Bond angle restraints: 6117 Sorted by residual: angle pdb=" C PRO A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N MET P 316 " pdb=" CA MET P 316 " pdb=" C MET P 316 " ideal model delta sigma weight residual 111.82 108.02 3.80 1.16e+00 7.43e-01 1.08e+01 angle pdb=" CA THR P 261 " pdb=" C THR P 261 " pdb=" O THR P 261 " ideal model delta sigma weight residual 121.87 118.14 3.73 1.16e+00 7.43e-01 1.03e+01 angle pdb=" N ILE P 69 " pdb=" CA ILE P 69 " pdb=" C ILE P 69 " ideal model delta sigma weight residual 111.48 108.48 3.00 9.40e-01 1.13e+00 1.02e+01 angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 113.18 119.11 -5.93 2.37e+00 1.78e-01 6.27e+00 ... (remaining 6112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2333 17.95 - 35.90: 207 35.90 - 53.84: 30 53.84 - 71.79: 3 71.79 - 89.74: 5 Dihedral angle restraints: 2578 sinusoidal: 984 harmonic: 1594 Sorted by residual: dihedral pdb=" CA ARG P 47 " pdb=" C ARG P 47 " pdb=" N PRO P 48 " pdb=" CA PRO P 48 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG P 151 " pdb=" C ARG P 151 " pdb=" N ARG P 152 " pdb=" CA ARG P 152 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PRO A 41 " pdb=" C PRO A 41 " pdb=" N GLU A 42 " pdb=" CA GLU A 42 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 582 0.059 - 0.119: 97 0.119 - 0.178: 11 0.178 - 0.238: 1 0.238 - 0.297: 1 Chirality restraints: 692 Sorted by residual: chirality pdb=" CA LEU P 318 " pdb=" N LEU P 318 " pdb=" C LEU P 318 " pdb=" CB LEU P 318 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PHE P 317 " pdb=" N PHE P 317 " pdb=" C PHE P 317 " pdb=" CB PHE P 317 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL P 279 " pdb=" CA VAL P 279 " pdb=" CG1 VAL P 279 " pdb=" CG2 VAL P 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 689 not shown) Planarity restraints: 765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 182 " 0.015 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP P 182 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP P 182 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 182 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 182 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 182 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 182 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR P 143 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO P 144 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO P 144 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO P 144 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 341 " -0.014 2.00e-02 2.50e+03 1.27e-02 2.80e+00 pdb=" CG PHE P 341 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE P 341 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE P 341 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE P 341 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE P 341 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE P 341 " -0.001 2.00e-02 2.50e+03 ... (remaining 762 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 390 2.74 - 3.28: 4352 3.28 - 3.82: 7394 3.82 - 4.36: 8374 4.36 - 4.90: 14840 Nonbonded interactions: 35350 Sorted by model distance: nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR P 281 " pdb=" OD2 ASP P 305 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 7 " pdb=" OG SER A 21 " model vdw 2.256 2.440 nonbonded pdb=" NE2 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.292 2.520 nonbonded pdb=" O PRO P 49 " pdb=" OH TYR A 100 " model vdw 2.298 2.440 ... (remaining 35345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 5.900 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.930 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 0.039 4485 Z= 0.225 Angle : 0.641 7.482 6117 Z= 0.347 Chirality : 0.046 0.297 692 Planarity : 0.004 0.047 765 Dihedral : 13.794 89.741 1554 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.62 (0.37), residues: 546 helix: 1.17 (0.38), residues: 199 sheet: -1.09 (0.44), residues: 150 loop : -1.41 (0.44), residues: 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.504 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1762 time to fit residues: 22.4260 Evaluate side-chains 83 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.0070 chunk 49 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 96 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 288 ASN P 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4485 Z= 0.235 Angle : 0.604 9.611 6117 Z= 0.304 Chirality : 0.043 0.147 692 Planarity : 0.004 0.045 765 Dihedral : 4.517 22.359 595 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.31 (0.38), residues: 546 helix: 1.65 (0.38), residues: 201 sheet: -1.07 (0.44), residues: 150 loop : -1.39 (0.45), residues: 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.449 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 95 average time/residue: 0.1523 time to fit residues: 18.5804 Evaluate side-chains 87 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0415 time to fit residues: 0.9472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4485 Z= 0.204 Angle : 0.568 7.459 6117 Z= 0.288 Chirality : 0.043 0.142 692 Planarity : 0.004 0.041 765 Dihedral : 4.403 21.939 595 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.19 (0.38), residues: 546 helix: 1.84 (0.38), residues: 200 sheet: -1.06 (0.43), residues: 150 loop : -1.38 (0.45), residues: 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.487 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.1549 time to fit residues: 18.2352 Evaluate side-chains 89 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0461 time to fit residues: 1.0299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 5 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 177 ASN P 189 GLN P 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4485 Z= 0.175 Angle : 0.548 6.564 6117 Z= 0.279 Chirality : 0.042 0.140 692 Planarity : 0.004 0.039 765 Dihedral : 4.305 21.484 595 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.11 (0.38), residues: 546 helix: 1.86 (0.38), residues: 200 sheet: -0.88 (0.46), residues: 141 loop : -1.40 (0.43), residues: 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.480 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.1567 time to fit residues: 19.4274 Evaluate side-chains 89 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0418 time to fit residues: 0.8057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 4485 Z= 0.334 Angle : 0.617 7.286 6117 Z= 0.312 Chirality : 0.045 0.157 692 Planarity : 0.004 0.039 765 Dihedral : 4.616 22.770 595 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.18 (0.38), residues: 546 helix: 1.87 (0.38), residues: 200 sheet: -0.91 (0.46), residues: 142 loop : -1.52 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.484 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 89 average time/residue: 0.1593 time to fit residues: 18.1328 Evaluate side-chains 84 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0435 time to fit residues: 1.2150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.0000 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4485 Z= 0.180 Angle : 0.558 6.940 6117 Z= 0.284 Chirality : 0.043 0.147 692 Planarity : 0.004 0.037 765 Dihedral : 4.394 21.861 595 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.12 (0.38), residues: 546 helix: 1.85 (0.38), residues: 200 sheet: -0.90 (0.47), residues: 142 loop : -1.39 (0.43), residues: 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.494 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.1688 time to fit residues: 19.9771 Evaluate side-chains 87 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0489 time to fit residues: 1.2253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4485 Z= 0.278 Angle : 0.594 7.158 6117 Z= 0.302 Chirality : 0.044 0.155 692 Planarity : 0.004 0.036 765 Dihedral : 4.542 22.401 595 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.16 (0.38), residues: 546 helix: 1.82 (0.38), residues: 200 sheet: -0.91 (0.47), residues: 142 loop : -1.42 (0.43), residues: 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.495 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 0.1647 time to fit residues: 17.9908 Evaluate side-chains 84 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0503 time to fit residues: 1.0392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4485 Z= 0.216 Angle : 0.576 7.577 6117 Z= 0.292 Chirality : 0.043 0.154 692 Planarity : 0.004 0.036 765 Dihedral : 4.475 22.006 595 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.13 (0.38), residues: 546 helix: 1.81 (0.38), residues: 200 sheet: -0.90 (0.47), residues: 142 loop : -1.36 (0.44), residues: 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.740 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.1737 time to fit residues: 18.8490 Evaluate side-chains 83 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0503 time to fit residues: 0.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8186 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 4485 Z= 0.211 Angle : 0.574 7.908 6117 Z= 0.290 Chirality : 0.043 0.163 692 Planarity : 0.004 0.036 765 Dihedral : 4.415 21.788 595 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.12 (0.38), residues: 546 helix: 1.82 (0.38), residues: 200 sheet: -0.90 (0.47), residues: 142 loop : -1.34 (0.44), residues: 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.526 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 0.1563 time to fit residues: 17.7095 Evaluate side-chains 88 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0427 time to fit residues: 0.6817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0970 chunk 33 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8183 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 4485 Z= 0.214 Angle : 0.587 7.983 6117 Z= 0.297 Chirality : 0.044 0.157 692 Planarity : 0.004 0.036 765 Dihedral : 4.418 21.711 595 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.15 (0.38), residues: 546 helix: 1.80 (0.38), residues: 200 sheet: -0.91 (0.47), residues: 142 loop : -1.36 (0.44), residues: 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.482 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.1594 time to fit residues: 18.5274 Evaluate side-chains 83 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0439 time to fit residues: 0.7411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0870 chunk 5 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.158728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.125305 restraints weight = 5181.547| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.11 r_work: 0.3248 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4485 Z= 0.188 Angle : 0.575 8.031 6117 Z= 0.291 Chirality : 0.043 0.160 692 Planarity : 0.004 0.036 765 Dihedral : 4.352 21.153 595 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.10 (0.39), residues: 546 helix: 1.83 (0.38), residues: 200 sheet: -0.89 (0.47), residues: 142 loop : -1.33 (0.44), residues: 204 =============================================================================== Job complete usr+sys time: 1351.88 seconds wall clock time: 25 minutes 3.84 seconds (1503.84 seconds total)