Starting phenix.real_space_refine on Wed Feb 14 14:57:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkd_12438/02_2024/7nkd_12438.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkd_12438/02_2024/7nkd_12438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkd_12438/02_2024/7nkd_12438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkd_12438/02_2024/7nkd_12438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkd_12438/02_2024/7nkd_12438.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkd_12438/02_2024/7nkd_12438.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians S 5 5.16 5 C 2952 2.51 5 N 852 2.21 5 O 978 1.98 5 H 4768 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 86": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "d GLU 355": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9555 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1346 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 6 Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 652 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 4 Chain: "C" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 448 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 2 Chain: "D" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 601 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain breaks: 3 Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 620 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain breaks: 3 Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 277 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain breaks: 3 Chain: "d" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5084 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 10, 'TRANS': 325} Chain: "b" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 527 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 4.90, per 1000 atoms: 0.51 Number of scatterers: 9555 At special positions: 0 Unit cell: (111.22, 73.04, 83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 5 16.00 O 978 8.00 N 852 7.00 C 2952 6.00 H 4768 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.05 Conformation dependent library (CDL) restraints added in 927.3 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 51.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.529A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.593A pdb=" N ALA B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'd' and resid 110 through 138 Processing helix chain 'd' and resid 139 through 157 removed outlier: 3.559A pdb=" N GLN d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 192 removed outlier: 3.729A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 225 Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.577A pdb=" N ASN d 259 " --> pdb=" O THR d 255 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 286 removed outlier: 3.882A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 Processing helix chain 'd' and resid 306 through 314 Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 3.742A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 412 through 416 Processing helix chain 'd' and resid 431 through 442 Processing helix chain 'b' and resid 131 through 145 Processing helix chain 'b' and resid 147 through 161 removed outlier: 3.557A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 5.782A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 5.926A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.476A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.466A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY D 58 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG D 63 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS D 56 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.268A pdb=" N HIS E 56 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 63 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4766 1.03 - 1.23: 2 1.23 - 1.42: 1901 1.42 - 1.61: 2901 1.61 - 1.81: 8 Bond restraints: 9578 Sorted by residual: bond pdb=" N THR d 166 " pdb=" CA THR d 166 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N ILE d 164 " pdb=" CA ILE d 164 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.13e+00 bond pdb=" CA ILE d 164 " pdb=" CB ILE d 164 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.42e-02 4.96e+03 6.61e-01 bond pdb=" C LEU d 416 " pdb=" N GLY d 417 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.46e-01 bond pdb=" C ASP d 412 " pdb=" O ASP d 412 " ideal model delta sigma weight residual 1.238 1.247 -0.009 1.28e-02 6.10e+03 5.13e-01 ... (remaining 9573 not shown) Histogram of bond angle deviations from ideal: 100.97 - 107.56: 390 107.56 - 114.16: 11775 114.16 - 120.76: 2997 120.76 - 127.35: 2122 127.35 - 133.95: 35 Bond angle restraints: 17319 Sorted by residual: angle pdb=" N ILE d 164 " pdb=" CA ILE d 164 " pdb=" C ILE d 164 " ideal model delta sigma weight residual 106.21 109.21 -3.00 1.07e+00 8.73e-01 7.87e+00 angle pdb=" C THR d 166 " pdb=" CA THR d 166 " pdb=" CB THR d 166 " ideal model delta sigma weight residual 110.42 115.69 -5.27 1.99e+00 2.53e-01 7.01e+00 angle pdb=" C SER C 21 " pdb=" N PHE C 22 " pdb=" CA PHE C 22 " ideal model delta sigma weight residual 122.56 118.63 3.93 1.72e+00 3.38e-01 5.21e+00 angle pdb=" CA GLY d 417 " pdb=" C GLY d 417 " pdb=" N GLY d 418 " ideal model delta sigma weight residual 115.34 116.84 -1.50 8.40e-01 1.42e+00 3.17e+00 angle pdb=" C ASP d 165 " pdb=" N THR d 166 " pdb=" CA THR d 166 " ideal model delta sigma weight residual 121.54 124.61 -3.07 1.91e+00 2.74e-01 2.58e+00 ... (remaining 17314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 3993 17.50 - 34.99: 301 34.99 - 52.49: 95 52.49 - 69.99: 22 69.99 - 87.48: 10 Dihedral angle restraints: 4421 sinusoidal: 2498 harmonic: 1923 Sorted by residual: dihedral pdb=" CB GLU C 12 " pdb=" CG GLU C 12 " pdb=" CD GLU C 12 " pdb=" OE1 GLU C 12 " ideal model delta sinusoidal sigma weight residual 0.00 -87.48 87.48 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP D 59 " pdb=" CB ASP D 59 " pdb=" CG ASP D 59 " pdb=" OD1 ASP D 59 " ideal model delta sinusoidal sigma weight residual -30.00 -84.12 54.12 1 2.00e+01 2.50e-03 9.93e+00 dihedral pdb=" CG ARG D 26 " pdb=" CD ARG D 26 " pdb=" NE ARG D 26 " pdb=" CZ ARG D 26 " ideal model delta sinusoidal sigma weight residual 180.00 138.41 41.59 2 1.50e+01 4.44e-03 9.40e+00 ... (remaining 4418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 535 0.026 - 0.053: 158 0.053 - 0.079: 53 0.079 - 0.105: 38 0.105 - 0.132: 18 Chirality restraints: 802 Sorted by residual: chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA VAL D 29 " pdb=" N VAL D 29 " pdb=" C VAL D 29 " pdb=" CB VAL D 29 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE d 428 " pdb=" N ILE d 428 " pdb=" C ILE d 428 " pdb=" CB ILE d 428 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 799 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 29 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" CD GLU A 29 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU A 29 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 29 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN b 136 " -0.005 2.00e-02 2.50e+03 9.30e-03 1.30e+00 pdb=" CD GLN b 136 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN b 136 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN b 136 " -0.009 2.00e-02 2.50e+03 pdb="HE21 GLN b 136 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN b 136 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 152 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.11e+00 pdb=" C SER b 152 " 0.018 2.00e-02 2.50e+03 pdb=" O SER b 152 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA b 153 " -0.006 2.00e-02 2.50e+03 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 651 2.20 - 2.80: 20245 2.80 - 3.40: 26639 3.40 - 4.00: 33554 4.00 - 4.60: 51795 Nonbonded interactions: 132884 Sorted by model distance: nonbonded pdb=" OE1 GLU B 71 " pdb=" H GLU B 71 " model vdw 1.596 1.850 nonbonded pdb=" OE1 GLU A 71 " pdb=" H GLU A 71 " model vdw 1.611 1.850 nonbonded pdb=" HG1 THR d 263 " pdb=" OD1 ASN d 266 " model vdw 1.616 1.850 nonbonded pdb=" HG SER d 179 " pdb=" O ARG d 260 " model vdw 1.638 1.850 nonbonded pdb=" O ARG F 11 " pdb=" H GLU F 23 " model vdw 1.647 1.850 ... (remaining 132879 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 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 30 or resid 55 through 81)) selection = (chain 'E' and (resid 8 through 15 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 21 \ through 30 or (resid 55 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HE21 or name HE22)) or resid 56 through 81)) } 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: 0.010 Normalize map: mean=0, sd=1: 5.850 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: 0.150 Extract box with map and model: 24.220 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 36.780 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.024 4810 Z= 0.172 Angle : 0.452 5.270 6490 Z= 0.252 Chirality : 0.037 0.132 802 Planarity : 0.003 0.032 848 Dihedral : 14.504 87.484 1754 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 2.45 (0.37), residues: 585 helix: 2.72 (0.30), residues: 314 sheet: -1.17 (0.70), residues: 57 loop : 0.90 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.001 0.000 HIS A 43 PHE 0.009 0.001 PHE d 187 TYR 0.006 0.001 TYR A 18 ARG 0.004 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2675 time to fit residues: 22.2550 Evaluate side-chains 49 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4810 Z= 0.285 Angle : 0.490 7.457 6490 Z= 0.265 Chirality : 0.039 0.136 802 Planarity : 0.003 0.027 848 Dihedral : 3.496 12.365 665 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.77 % Allowed : 3.47 % Favored : 95.75 % 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: 2.41 (0.36), residues: 585 helix: 2.85 (0.28), residues: 317 sheet: -1.10 (0.67), residues: 57 loop : 0.50 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.014 0.001 PHE C 22 TYR 0.005 0.001 TYR B 18 ARG 0.003 0.000 ARG d 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.1988 time to fit residues: 15.2478 Evaluate side-chains 50 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 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: 0.8205 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4810 Z= 0.222 Angle : 0.455 6.272 6490 Z= 0.243 Chirality : 0.038 0.136 802 Planarity : 0.003 0.025 848 Dihedral : 3.462 12.047 665 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.77 % Allowed : 5.41 % Favored : 93.82 % 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: 2.65 (0.36), residues: 585 helix: 3.09 (0.29), residues: 317 sheet: -1.02 (0.65), residues: 57 loop : 0.55 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.014 0.001 PHE C 22 TYR 0.009 0.001 TYR B 18 ARG 0.003 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.2043 time to fit residues: 15.3472 Evaluate side-chains 51 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8230 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4810 Z= 0.313 Angle : 0.487 5.941 6490 Z= 0.262 Chirality : 0.039 0.139 802 Planarity : 0.003 0.027 848 Dihedral : 3.542 12.925 665 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.77 % Allowed : 6.56 % Favored : 92.66 % 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: 2.48 (0.35), residues: 585 helix: 2.97 (0.28), residues: 318 sheet: -0.99 (0.65), residues: 57 loop : 0.38 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.015 0.001 PHE C 22 TYR 0.009 0.001 TYR B 18 ARG 0.003 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1981 time to fit residues: 14.9233 Evaluate side-chains 51 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4810 Z= 0.189 Angle : 0.444 5.848 6490 Z= 0.235 Chirality : 0.038 0.137 802 Planarity : 0.003 0.026 848 Dihedral : 3.453 12.222 665 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.77 % Allowed : 7.34 % Favored : 91.89 % 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: 2.79 (0.36), residues: 585 helix: 3.22 (0.29), residues: 317 sheet: -0.91 (0.65), residues: 57 loop : 0.56 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 261 HIS 0.002 0.000 HIS A 43 PHE 0.015 0.001 PHE C 22 TYR 0.008 0.001 TYR B 18 ARG 0.002 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.767 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.2031 time to fit residues: 15.8174 Evaluate side-chains 50 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4810 Z= 0.220 Angle : 0.456 5.674 6490 Z= 0.241 Chirality : 0.038 0.134 802 Planarity : 0.003 0.025 848 Dihedral : 3.429 12.409 665 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.58 % Allowed : 8.69 % Favored : 90.73 % 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: 2.77 (0.36), residues: 585 helix: 3.18 (0.29), residues: 317 sheet: -0.82 (0.65), residues: 57 loop : 0.55 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.014 0.001 PHE C 22 TYR 0.008 0.001 TYR B 18 ARG 0.003 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.2037 time to fit residues: 14.9950 Evaluate side-chains 48 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain C residue 22 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8239 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4810 Z= 0.334 Angle : 0.499 6.685 6490 Z= 0.267 Chirality : 0.039 0.140 802 Planarity : 0.003 0.025 848 Dihedral : 3.578 13.336 665 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.58 % Allowed : 9.27 % Favored : 90.15 % 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: 2.47 (0.35), residues: 585 helix: 2.95 (0.28), residues: 318 sheet: -0.82 (0.65), residues: 57 loop : 0.35 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.014 0.001 PHE C 22 TYR 0.008 0.002 TYR B 18 ARG 0.003 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8152 (tp30) cc_final: 0.7646 (tp30) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.2349 time to fit residues: 16.6400 Evaluate side-chains 48 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain C residue 22 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 0.0770 chunk 53 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4810 Z= 0.142 Angle : 0.442 7.250 6490 Z= 0.230 Chirality : 0.038 0.137 802 Planarity : 0.002 0.023 848 Dihedral : 3.418 12.217 665 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.77 % Allowed : 9.65 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.36), residues: 585 helix: 3.38 (0.29), residues: 317 sheet: -0.68 (0.65), residues: 57 loop : 0.60 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.001 0.000 HIS d 273 PHE 0.014 0.001 PHE C 22 TYR 0.006 0.001 TYR B 18 ARG 0.002 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8093 (tp30) cc_final: 0.7612 (tp30) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.2049 time to fit residues: 15.2139 Evaluate side-chains 48 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 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: 0.8216 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4810 Z= 0.212 Angle : 0.455 6.716 6490 Z= 0.240 Chirality : 0.038 0.133 802 Planarity : 0.003 0.023 848 Dihedral : 3.391 12.504 665 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.39 % Allowed : 10.23 % Favored : 89.38 % 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: 2.93 (0.36), residues: 585 helix: 3.32 (0.29), residues: 317 sheet: -0.61 (0.66), residues: 57 loop : 0.56 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.010 0.001 PHE d 187 TYR 0.007 0.001 TYR B 18 ARG 0.002 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8091 (tp30) cc_final: 0.7611 (tp30) outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.2018 time to fit residues: 14.5923 Evaluate side-chains 47 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4810 Z= 0.155 Angle : 0.440 7.071 6490 Z= 0.229 Chirality : 0.038 0.135 802 Planarity : 0.002 0.022 848 Dihedral : 3.304 11.990 665 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.39 % Allowed : 10.23 % Favored : 89.38 % 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: 3.10 (0.36), residues: 585 helix: 3.44 (0.29), residues: 317 sheet: -0.52 (0.67), residues: 57 loop : 0.67 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.001 0.000 HIS d 378 PHE 0.008 0.001 PHE d 187 TYR 0.005 0.001 TYR B 18 ARG 0.002 0.000 ARG D 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8057 (tp30) cc_final: 0.7523 (tp30) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.2282 time to fit residues: 16.9827 Evaluate side-chains 48 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.073251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057605 restraints weight = 41592.966| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.37 r_work: 0.2961 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4810 Z= 0.234 Angle : 0.460 6.477 6490 Z= 0.243 Chirality : 0.038 0.134 802 Planarity : 0.003 0.023 848 Dihedral : 3.347 12.527 665 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.39 % Allowed : 10.62 % Favored : 89.00 % 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: 2.89 (0.36), residues: 585 helix: 3.34 (0.28), residues: 317 sheet: -0.59 (0.63), residues: 62 loop : 0.48 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.010 0.001 PHE d 187 TYR 0.006 0.001 TYR B 18 ARG 0.003 0.000 ARG D 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.24 seconds wall clock time: 55 minutes 2.69 seconds (3302.69 seconds total)