Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 18:08:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/07_2023/8bdz_15995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/07_2023/8bdz_15995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/07_2023/8bdz_15995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/07_2023/8bdz_15995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/07_2023/8bdz_15995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/07_2023/8bdz_15995.pdb" } resolution = 3.13 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= 0.063 sd= 0.372 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 18 5.16 5 C 2157 2.51 5 N 546 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 30": "OD1" <-> "OD2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C ASP 223": "OD1" <-> "OD2" 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: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 2.12, per 1000 atoms: 0.64 Number of scatterers: 3309 At special positions: 0 Unit cell: (87.4532, 76.3832, 91.8812, 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 18 16.00 O 588 8.00 N 546 7.00 C 2157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 59 " 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: 1.40 Conformation dependent library (CDL) restraints added in 483.8 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.600A pdb=" N GLY A 8 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 16 through 17 No H-bonds generated for 'chain 'A' and resid 16 through 17' Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.724A pdb=" N PHE A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.911A pdb=" N ARG A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.604A pdb=" N THR A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.918A pdb=" N ASN A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.606A pdb=" N PHE B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 6.296A pdb=" N ASP B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.784A pdb=" N ARG B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.530A pdb=" N THR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.837A pdb=" N VAL B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.891A pdb=" N PHE C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 6.033A pdb=" N ASP C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 42 removed outlier: 3.875A pdb=" N ARG C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 222 through 230 removed outlier: 4.111A pdb=" N VAL C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.789A pdb=" N LYS C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 269 through 273 218 hydrogen bonds defined for protein. 618 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: 0.79 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1032 1.35 - 1.46: 865 1.46 - 1.58: 1487 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 3411 Sorted by residual: bond pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.33e-01 bond pdb=" CD GLU C 257 " pdb=" OE1 GLU C 257 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.43e-01 bond pdb=" CD GLU B 257 " pdb=" OE1 GLU B 257 " ideal model delta sigma weight residual 1.249 1.234 0.015 1.90e-02 2.77e+03 6.64e-01 bond pdb=" CA CYS B 46 " pdb=" CB CYS B 46 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.91e-01 bond pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.34e-01 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.27: 155 106.27 - 113.19: 1833 113.19 - 120.12: 1185 120.12 - 127.04: 1425 127.04 - 133.96: 64 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C HIS B 45 " pdb=" N CYS B 46 " pdb=" CA CYS B 46 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta sigma weight residual 110.39 114.79 -4.40 1.66e+00 3.63e-01 7.02e+00 angle pdb=" C HIS C 45 " pdb=" N CYS C 46 " pdb=" CA CYS C 46 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" CB GLU B 257 " ideal model delta sigma weight residual 110.28 114.08 -3.80 1.55e+00 4.16e-01 6.00e+00 angle pdb=" C ILE A 256 " pdb=" N GLU A 257 " pdb=" CA GLU A 257 " ideal model delta sigma weight residual 120.72 116.80 3.92 1.67e+00 3.59e-01 5.51e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.27: 1722 12.27 - 24.53: 194 24.53 - 36.80: 61 36.80 - 49.06: 18 49.06 - 61.32: 6 Dihedral angle restraints: 2001 sinusoidal: 792 harmonic: 1209 Sorted by residual: dihedral pdb=" CA ASP A 2 " pdb=" CB ASP A 2 " pdb=" CG ASP A 2 " pdb=" OD1 ASP A 2 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 118.39 -25.39 1 1.00e+01 1.00e-02 9.27e+00 dihedral pdb=" CA SER A 47 " pdb=" C SER A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.99e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 395 0.037 - 0.074: 104 0.074 - 0.112: 22 0.112 - 0.149: 2 0.149 - 0.186: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA GLU C 257 " pdb=" N GLU C 257 " pdb=" C GLU C 257 " pdb=" CB GLU C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 522 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 253 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C GLU B 253 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU B 253 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 254 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 268 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 269 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 45 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C HIS C 45 " -0.023 2.00e-02 2.50e+03 pdb=" O HIS C 45 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS C 46 " 0.008 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 825 2.79 - 3.32: 3428 3.32 - 3.85: 5678 3.85 - 4.37: 6494 4.37 - 4.90: 11051 Nonbonded interactions: 27476 Sorted by model distance: nonbonded pdb=" OG SER C 47 " pdb=" ND1 HIS C 50 " model vdw 2.264 2.520 nonbonded pdb=" OG SER B 47 " pdb=" ND1 HIS B 50 " model vdw 2.300 2.520 nonbonded pdb=" O PHE A 22 " pdb=" NH2 ARG A 238 " model vdw 2.301 2.520 nonbonded pdb=" O GLU A 62 " pdb=" OG1 THR A 65 " model vdw 2.302 2.440 nonbonded pdb=" OE2 GLU A 62 " pdb=" NZ LYS B 236 " model vdw 2.319 2.520 ... (remaining 27471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.160 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: 17.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.002 0.022 3411 Z= 0.142 Angle : 0.522 6.373 4662 Z= 0.279 Chirality : 0.037 0.186 525 Planarity : 0.004 0.033 585 Dihedral : 12.414 61.325 1212 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.43), residues: 402 helix: 1.50 (0.31), residues: 291 sheet: None (None), residues: 0 loop : 1.86 (0.65), residues: 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2339 time to fit residues: 11.5044 Evaluate side-chains 27 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3411 Z= 0.189 Angle : 0.537 4.793 4662 Z= 0.279 Chirality : 0.038 0.151 525 Planarity : 0.004 0.036 585 Dihedral : 3.877 13.481 447 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.43), residues: 402 helix: 1.84 (0.31), residues: 292 sheet: None (None), residues: 0 loop : 1.97 (0.63), residues: 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.1703 time to fit residues: 6.5993 Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0464 time to fit residues: 0.7752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3411 Z= 0.268 Angle : 0.535 4.051 4662 Z= 0.278 Chirality : 0.038 0.113 525 Planarity : 0.004 0.035 585 Dihedral : 3.886 14.892 447 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.42), residues: 402 helix: 1.93 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.91 (0.64), residues: 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.398 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.1855 time to fit residues: 6.7897 Evaluate side-chains 27 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 3411 Z= 0.400 Angle : 0.594 4.474 4662 Z= 0.307 Chirality : 0.042 0.122 525 Planarity : 0.005 0.039 585 Dihedral : 4.150 18.203 447 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.41), residues: 402 helix: 1.86 (0.29), residues: 292 sheet: None (None), residues: 0 loop : 1.66 (0.62), residues: 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.350 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.1670 time to fit residues: 6.7285 Evaluate side-chains 31 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0470 time to fit residues: 0.6820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3411 Z= 0.200 Angle : 0.508 4.597 4662 Z= 0.265 Chirality : 0.037 0.111 525 Planarity : 0.004 0.038 585 Dihedral : 3.979 17.699 447 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.42), residues: 402 helix: 1.99 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.76 (0.63), residues: 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.380 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.1609 time to fit residues: 7.0378 Evaluate side-chains 31 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0438 time to fit residues: 0.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3411 Z= 0.186 Angle : 0.517 6.574 4662 Z= 0.266 Chirality : 0.036 0.127 525 Planarity : 0.004 0.034 585 Dihedral : 3.879 17.016 447 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.42), residues: 402 helix: 2.09 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.89 (0.64), residues: 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.402 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.1597 time to fit residues: 6.7747 Evaluate side-chains 31 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0410 time to fit residues: 0.5960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3411 Z= 0.212 Angle : 0.536 6.252 4662 Z= 0.277 Chirality : 0.036 0.118 525 Planarity : 0.004 0.033 585 Dihedral : 3.896 16.957 447 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.42), residues: 402 helix: 2.10 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.92 (0.64), residues: 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.403 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.1909 time to fit residues: 7.1228 Evaluate side-chains 29 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4601 time to fit residues: 1.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 3411 Z= 0.250 Angle : 0.551 6.591 4662 Z= 0.284 Chirality : 0.037 0.121 525 Planarity : 0.005 0.037 585 Dihedral : 3.933 17.299 447 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.42), residues: 402 helix: 2.08 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.87 (0.63), residues: 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.399 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.1860 time to fit residues: 7.8384 Evaluate side-chains 30 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0441 time to fit residues: 0.5864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3411 Z= 0.251 Angle : 0.566 6.814 4662 Z= 0.295 Chirality : 0.037 0.121 525 Planarity : 0.005 0.054 585 Dihedral : 3.965 17.577 447 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.42), residues: 402 helix: 2.07 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.85 (0.63), residues: 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.383 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.1671 time to fit residues: 6.6725 Evaluate side-chains 30 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0393 time to fit residues: 0.5900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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: 0.8299 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 3411 Z= 0.149 Angle : 0.528 6.795 4662 Z= 0.270 Chirality : 0.034 0.116 525 Planarity : 0.004 0.032 585 Dihedral : 3.757 15.563 447 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.43), residues: 402 helix: 2.17 (0.31), residues: 292 sheet: None (None), residues: 0 loop : 2.07 (0.64), residues: 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.380 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.2078 time to fit residues: 8.7709 Evaluate side-chains 31 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.054724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044589 restraints weight = 16328.922| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.75 r_work: 0.2960 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3411 Z= 0.224 Angle : 0.561 7.438 4662 Z= 0.291 Chirality : 0.037 0.155 525 Planarity : 0.004 0.037 585 Dihedral : 3.770 15.940 447 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.43), residues: 402 helix: 2.15 (0.31), residues: 292 sheet: None (None), residues: 0 loop : 2.00 (0.63), residues: 110 =============================================================================== Job complete usr+sys time: 1032.08 seconds wall clock time: 19 minutes 26.19 seconds (1166.19 seconds total)