Starting phenix.real_space_refine on Fri Mar 14 04:16:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkd_12438/03_2025/7nkd_12438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkd_12438/03_2025/7nkd_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/cci-nas-00/data/ceres_data/7nkd_12438/03_2025/7nkd_12438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkd_12438/03_2025/7nkd_12438.map" model { file = "/net/cci-nas-00/data/ceres_data/7nkd_12438/03_2025/7nkd_12438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkd_12438/03_2025/7nkd_12438.cif" } 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. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 13.65, per 1000 atoms: 1.43 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 7.42 Time building geometry restraints manager: 3.64 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: 0.00 - 1.05: 16447 1.05 - 2.11: 831 2.11 - 3.16: 24 3.16 - 4.22: 16 4.22 - 5.27: 1 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 2.450 nonbonded pdb=" OE1 GLU A 71 " pdb=" H GLU A 71 " model vdw 1.611 2.450 nonbonded pdb=" HG1 THR d 263 " pdb=" OD1 ASN d 266 " model vdw 1.616 2.450 nonbonded pdb=" HG SER d 179 " pdb=" O ARG d 260 " model vdw 1.638 2.450 nonbonded pdb=" O ARG F 11 " pdb=" H GLU F 23 " model vdw 1.647 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 849.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 40.030 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 899.210 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3253 time to fit residues: 27.0670 Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.3980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.073149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057593 restraints weight = 41498.144| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.38 r_work: 0.2966 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0916 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= 0.280 Angle : 0.508 8.294 6490 Z= 0.273 Chirality : 0.039 0.137 802 Planarity : 0.003 0.030 848 Dihedral : 3.516 13.181 665 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.58 % Allowed : 3.86 % Favored : 95.56 % 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: 2.38 (0.35), residues: 585 helix: 2.87 (0.28), residues: 317 sheet: -1.11 (0.67), residues: 57 loop : 0.41 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.001 0.000 HIS C 72 PHE 0.014 0.001 PHE C 22 TYR 0.007 0.001 TYR B 18 ARG 0.003 0.000 ARG d 115 *********************** 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 53 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.2099 time to fit residues: 16.6717 Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.073508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058325 restraints weight = 41774.922| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.33 r_work: 0.2972 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4810 Z= 0.225 Angle : 0.467 6.640 6490 Z= 0.250 Chirality : 0.039 0.136 802 Planarity : 0.003 0.027 848 Dihedral : 3.472 13.142 665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.58 % Allowed : 5.41 % Favored : 94.02 % 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: 2.59 (0.36), residues: 585 helix: 3.12 (0.29), residues: 317 sheet: -1.06 (0.65), residues: 57 loop : 0.38 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 261 HIS 0.002 0.000 HIS d 410 PHE 0.014 0.001 PHE C 22 TYR 0.008 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** 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 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8416 (tp30) cc_final: 0.8116 (tp30) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1963 time to fit residues: 14.1470 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.072654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.057187 restraints weight = 41561.200| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.35 r_work: 0.2952 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4810 Z= 0.277 Angle : 0.478 5.939 6490 Z= 0.256 Chirality : 0.039 0.136 802 Planarity : 0.003 0.033 848 Dihedral : 3.503 13.522 665 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.39 % Allowed : 6.95 % 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: 2.51 (0.35), residues: 585 helix: 3.08 (0.29), residues: 317 sheet: -1.05 (0.64), residues: 57 loop : 0.29 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.002 0.001 HIS d 410 PHE 0.014 0.001 PHE C 22 TYR 0.009 0.001 TYR B 18 ARG 0.003 0.000 ARG d 115 *********************** 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 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8435 (tp30) cc_final: 0.8124 (tp30) outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.2023 time to fit residues: 14.4869 Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.073282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058141 restraints weight = 41512.164| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.27 r_work: 0.2966 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4810 Z= 0.198 Angle : 0.450 5.590 6490 Z= 0.239 Chirality : 0.038 0.137 802 Planarity : 0.003 0.036 848 Dihedral : 3.424 13.012 665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.39 % Allowed : 7.34 % Favored : 92.28 % 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: 2.72 (0.36), residues: 585 helix: 3.23 (0.29), residues: 317 sheet: -0.96 (0.64), residues: 57 loop : 0.40 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.002 0.000 HIS d 378 PHE 0.014 0.001 PHE C 22 TYR 0.007 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** 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 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8627 (p0) cc_final: 0.8379 (p0) REVERT: A 43 HIS cc_start: 0.8532 (m90) cc_final: 0.8260 (m90) REVERT: F 23 GLU cc_start: 0.8422 (tp30) cc_final: 0.8106 (tp30) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.2081 time to fit residues: 15.3577 Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.072905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057258 restraints weight = 41574.010| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.36 r_work: 0.2946 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4810 Z= 0.270 Angle : 0.471 5.078 6490 Z= 0.253 Chirality : 0.039 0.135 802 Planarity : 0.003 0.036 848 Dihedral : 3.453 13.488 665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.39 % Allowed : 8.88 % 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: 2.63 (0.35), residues: 585 helix: 3.16 (0.28), residues: 317 sheet: -0.92 (0.65), residues: 57 loop : 0.33 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.002 0.001 HIS d 378 PHE 0.014 0.001 PHE C 22 TYR 0.008 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** 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 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8602 (p0) cc_final: 0.8318 (p0) REVERT: A 43 HIS cc_start: 0.8588 (m90) cc_final: 0.8291 (m90) REVERT: F 23 GLU cc_start: 0.8406 (tp30) cc_final: 0.8093 (tp30) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.2074 time to fit residues: 15.4724 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.072978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057384 restraints weight = 41526.133| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.38 r_work: 0.2961 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4810 Z= 0.205 Angle : 0.460 7.877 6490 Z= 0.242 Chirality : 0.039 0.135 802 Planarity : 0.003 0.036 848 Dihedral : 3.404 13.078 665 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.19 % Allowed : 9.07 % 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: 2.78 (0.36), residues: 585 helix: 3.26 (0.29), residues: 317 sheet: -0.83 (0.65), residues: 57 loop : 0.43 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.002 0.000 HIS d 378 PHE 0.014 0.001 PHE C 22 TYR 0.006 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** 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 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8590 (p0) cc_final: 0.8286 (p0) REVERT: A 43 HIS cc_start: 0.8574 (m90) cc_final: 0.8278 (m90) REVERT: F 23 GLU cc_start: 0.8407 (tp30) cc_final: 0.8091 (tp30) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.2258 time to fit residues: 15.9876 Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.073143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057374 restraints weight = 42242.977| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.43 r_work: 0.2957 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1581 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= 0.203 Angle : 0.457 7.816 6490 Z= 0.240 Chirality : 0.038 0.135 802 Planarity : 0.003 0.036 848 Dihedral : 3.381 13.120 665 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % 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: 2.85 (0.36), residues: 585 helix: 3.32 (0.29), residues: 317 sheet: -0.76 (0.66), residues: 57 loop : 0.45 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.002 0.000 HIS d 378 PHE 0.009 0.001 PHE d 187 TYR 0.006 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** 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 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8596 (p0) cc_final: 0.8298 (p0) REVERT: A 43 HIS cc_start: 0.8572 (m90) cc_final: 0.8281 (m90) REVERT: F 23 GLU cc_start: 0.8407 (tp30) cc_final: 0.7738 (tp30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1926 time to fit residues: 13.6773 Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 0.0980 chunk 3 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.073558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058054 restraints weight = 41481.198| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.36 r_work: 0.2980 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1633 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= 0.137 Angle : 0.442 8.718 6490 Z= 0.228 Chirality : 0.038 0.136 802 Planarity : 0.003 0.036 848 Dihedral : 3.273 12.416 665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % 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: 3.04 (0.36), residues: 585 helix: 3.46 (0.29), residues: 317 sheet: -0.67 (0.66), residues: 57 loop : 0.57 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.001 0.000 HIS d 222 PHE 0.008 0.001 PHE d 187 TYR 0.005 0.001 TYR A 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 to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8397 (tp30) cc_final: 0.7756 (tp30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2399 time to fit residues: 17.3199 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 41 optimal weight: 0.0980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.073408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057895 restraints weight = 41848.066| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.37 r_work: 0.2972 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1669 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 : 0.449 8.793 6490 Z= 0.232 Chirality : 0.038 0.136 802 Planarity : 0.003 0.036 848 Dihedral : 3.231 12.565 665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.19 % Allowed : 9.65 % 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: 3.08 (0.36), residues: 585 helix: 3.46 (0.29), residues: 317 sheet: -0.56 (0.66), residues: 57 loop : 0.59 (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 0.009 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 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8642 (p0) cc_final: 0.8406 (p0) REVERT: A 43 HIS cc_start: 0.8569 (m90) cc_final: 0.8331 (m90) REVERT: F 23 GLU cc_start: 0.8393 (tp30) cc_final: 0.7760 (tp30) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.2036 time to fit residues: 15.0658 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.073252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057623 restraints weight = 41738.551| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.38 r_work: 0.2966 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1694 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= 0.205 Angle : 0.460 8.637 6490 Z= 0.240 Chirality : 0.038 0.135 802 Planarity : 0.003 0.035 848 Dihedral : 3.264 12.741 665 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 9.85 % 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: 3.02 (0.36), residues: 585 helix: 3.43 (0.29), residues: 317 sheet: -0.55 (0.67), residues: 57 loop : 0.54 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.002 0.000 HIS d 378 PHE 0.009 0.001 PHE d 187 TYR 0.006 0.001 TYR B 18 ARG 0.002 0.000 ARG D 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6320.52 seconds wall clock time: 111 minutes 7.40 seconds (6667.40 seconds total)