Starting phenix.real_space_refine on Mon Jul 28 18:01:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkq_12446/07_2025/7nkq_12446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkq_12446/07_2025/7nkq_12446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nkq_12446/07_2025/7nkq_12446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkq_12446/07_2025/7nkq_12446.map" model { file = "/net/cci-nas-00/data/ceres_data/7nkq_12446/07_2025/7nkq_12446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkq_12446/07_2025/7nkq_12446.cif" } resolution = 2.98 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= 0.001 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 7 5.16 5 C 3278 2.51 5 N 946 2.21 5 O 1078 1.98 5 H 5312 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10621 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1500 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 917 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain breaks: 3 Chain: "C" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 643 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain breaks: 3 Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 752 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 4 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 721 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain breaks: 2 Chain: "F" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 559 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 3 Chain: "d" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5002 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 10, 'TRANS': 319} Chain breaks: 1 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: 7.91, per 1000 atoms: 0.74 Number of scatterers: 10621 At special positions: 0 Unit cell: (112.05, 77.19, 83.83, 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 7 16.00 O 1078 8.00 N 946 7.00 C 3278 6.00 H 5312 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: 3.02 Conformation dependent library (CDL) restraints added in 733.7 milliseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 41.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 4.189A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'B' and resid 9 through 21 removed outlier: 3.745A pdb=" N ILE B 15 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'd' and resid 110 through 137 Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 190 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 222 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.876A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 313 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 371 Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 Processing helix chain 'b' and resid 131 through 160 removed outlier: 3.611A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 591 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: 3.31 Time building geometry restraints manager: 3.63 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: 5310 1.03 - 1.23: 6 1.23 - 1.42: 2098 1.42 - 1.61: 3226 1.61 - 1.81: 12 Bond restraints: 10652 Sorted by residual: bond pdb=" CA ARG E 63 " pdb=" CB ARG E 63 " ideal model delta sigma weight residual 1.528 1.502 0.027 2.61e-02 1.47e+03 1.05e+00 bond pdb=" CG GLU d 155 " pdb=" CD GLU d 155 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.23e-01 bond pdb=" CB ARG E 14 " pdb=" CG ARG E 14 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.20e-01 bond pdb=" CB ASP A 70 " pdb=" CG ASP A 70 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 bond pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.86e-01 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 17233 0.83 - 1.66: 1876 1.66 - 2.48: 134 2.48 - 3.31: 20 3.31 - 4.14: 19 Bond angle restraints: 19282 Sorted by residual: angle pdb=" N GLU d 155 " pdb=" CA GLU d 155 " pdb=" CB GLU d 155 " ideal model delta sigma weight residual 110.12 114.15 -4.03 1.47e+00 4.63e-01 7.51e+00 angle pdb=" N GLU d 205 " pdb=" CA GLU d 205 " pdb=" CB GLU d 205 " ideal model delta sigma weight residual 110.12 113.26 -3.14 1.47e+00 4.63e-01 4.56e+00 angle pdb=" C LEU d 154 " pdb=" N GLU d 155 " pdb=" CA GLU d 155 " ideal model delta sigma weight residual 120.28 117.83 2.45 1.34e+00 5.57e-01 3.36e+00 angle pdb=" CA GLN d 112 " pdb=" CB GLN d 112 " pdb=" CG GLN d 112 " ideal model delta sigma weight residual 114.10 117.74 -3.64 2.00e+00 2.50e-01 3.32e+00 angle pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " pdb=" CD GLU C 16 " ideal model delta sigma weight residual 112.60 115.61 -3.01 1.70e+00 3.46e-01 3.14e+00 ... (remaining 19277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4359 16.36 - 32.72: 406 32.72 - 49.08: 95 49.08 - 65.44: 44 65.44 - 81.80: 7 Dihedral angle restraints: 4911 sinusoidal: 2783 harmonic: 2128 Sorted by residual: dihedral pdb=" CA LEU d 409 " pdb=" C LEU d 409 " pdb=" N HIS d 410 " pdb=" CA HIS d 410 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP d 197 " pdb=" CB ASP d 197 " pdb=" CG ASP d 197 " pdb=" OD1 ASP d 197 " ideal model delta sinusoidal sigma weight residual -30.00 -88.29 58.29 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP b 163 " pdb=" CB ASP b 163 " pdb=" CG ASP b 163 " pdb=" OD1 ASP b 163 " ideal model delta sinusoidal sigma weight residual -30.00 -86.06 56.06 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 559 0.027 - 0.054: 197 0.054 - 0.082: 63 0.082 - 0.109: 45 0.109 - 0.136: 28 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA VAL B 74 " pdb=" N VAL B 74 " pdb=" C VAL B 74 " pdb=" CB VAL B 74 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA GLU C 16 " pdb=" N GLU C 16 " pdb=" C GLU C 16 " pdb=" CB GLU C 16 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-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 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 889 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP d 269 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASP d 269 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP d 269 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA d 270 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN d 112 " -0.006 2.00e-02 2.50e+03 1.07e-02 1.70e+00 pdb=" CD GLN d 112 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN d 112 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN d 112 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN d 112 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN d 112 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 275 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C ALA d 275 " 0.022 2.00e-02 2.50e+03 pdb=" O ALA d 275 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG d 276 " -0.007 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 583 2.18 - 2.79: 22145 2.79 - 3.39: 30036 3.39 - 4.00: 38130 4.00 - 4.60: 58562 Nonbonded interactions: 149456 Sorted by model distance: nonbonded pdb=" O SER A 20 " pdb="HH12 ARG b 158 " model vdw 1.575 2.450 nonbonded pdb=" O ASN B 68 " pdb=" H GLY B 75 " model vdw 1.602 2.450 nonbonded pdb=" H ALA D 54 " pdb=" O ARG D 63 " model vdw 1.604 2.450 nonbonded pdb=" HH TYR d 401 " pdb=" OE1 GLU d 426 " model vdw 1.605 2.450 nonbonded pdb=" O GLU d 225 " pdb=" HZ1 LYS d 233 " model vdw 1.611 2.450 ... (remaining 149451 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 229.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 271.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.004 0.029 5340 Z= 0.188 Angle : 0.490 4.141 7215 Z= 0.264 Chirality : 0.041 0.136 892 Planarity : 0.003 0.033 945 Dihedral : 13.517 81.800 1951 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.39 (0.34), residues: 662 helix: 1.88 (0.30), residues: 311 sheet: -0.90 (0.53), residues: 85 loop : 0.56 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.010 0.001 PHE d 150 TYR 0.011 0.002 TYR C 18 ARG 0.007 0.000 ARG d 118 Details of bonding type rmsd hydrogen bonds : bond 0.06304 ( 206) hydrogen bonds : angle 4.69352 ( 591) covalent geometry : bond 0.00411 ( 5340) covalent geometry : angle 0.48964 ( 7215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 3.579 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7632 (t0) cc_final: 0.7398 (t0) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 2.8043 time to fit residues: 217.0764 Evaluate side-chains 51 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073785 restraints weight = 32091.909| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.99 r_work: 0.3081 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5340 Z= 0.153 Angle : 0.484 5.019 7215 Z= 0.255 Chirality : 0.040 0.136 892 Planarity : 0.004 0.045 945 Dihedral : 3.749 18.181 745 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.35 % Allowed : 8.54 % Favored : 91.11 % 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: 1.69 (0.34), residues: 662 helix: 2.26 (0.30), residues: 311 sheet: -1.32 (0.55), residues: 76 loop : 0.66 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS d 410 PHE 0.009 0.001 PHE d 187 TYR 0.010 0.002 TYR C 18 ARG 0.009 0.001 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 206) hydrogen bonds : angle 3.73163 ( 591) covalent geometry : bond 0.00334 ( 5340) covalent geometry : angle 0.48364 ( 7215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.8047 (t0) cc_final: 0.7637 (t0) REVERT: F 78 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7789 (mp0) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 1.9104 time to fit residues: 111.6032 Evaluate side-chains 51 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.100889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073146 restraints weight = 32268.258| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.01 r_work: 0.3060 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5340 Z= 0.187 Angle : 0.476 5.386 7215 Z= 0.248 Chirality : 0.040 0.130 892 Planarity : 0.004 0.069 945 Dihedral : 3.683 18.269 743 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.17 % Allowed : 9.93 % Favored : 89.90 % 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: 1.68 (0.34), residues: 662 helix: 2.34 (0.29), residues: 312 sheet: -1.51 (0.55), residues: 76 loop : 0.60 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS d 410 PHE 0.009 0.001 PHE d 187 TYR 0.009 0.002 TYR d 316 ARG 0.009 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 206) hydrogen bonds : angle 3.63917 ( 591) covalent geometry : bond 0.00407 ( 5340) covalent geometry : angle 0.47578 ( 7215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.8016 (t0) cc_final: 0.7598 (t0) REVERT: F 78 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7853 (mp0) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 2.1287 time to fit residues: 118.6608 Evaluate side-chains 49 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 4 optimal weight: 0.3980 chunk 51 optimal weight: 0.0970 chunk 27 optimal weight: 0.0770 chunk 20 optimal weight: 0.2980 overall best weight: 0.1936 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.102371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074701 restraints weight = 32176.658| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.02 r_work: 0.3089 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5340 Z= 0.097 Angle : 0.438 4.847 7215 Z= 0.226 Chirality : 0.040 0.131 892 Planarity : 0.004 0.065 945 Dihedral : 3.431 16.964 743 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.87 % Allowed : 10.10 % Favored : 89.02 % 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: 1.86 (0.35), residues: 662 helix: 2.55 (0.30), residues: 312 sheet: -1.61 (0.55), residues: 76 loop : 0.67 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.000 HIS E 56 PHE 0.008 0.001 PHE d 150 TYR 0.007 0.002 TYR B 18 ARG 0.008 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 206) hydrogen bonds : angle 3.36499 ( 591) covalent geometry : bond 0.00219 ( 5340) covalent geometry : angle 0.43814 ( 7215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7943 (t0) cc_final: 0.7471 (t0) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 2.3511 time to fit residues: 151.5782 Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073313 restraints weight = 32074.859| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.00 r_work: 0.3063 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5340 Z= 0.181 Angle : 0.475 5.128 7215 Z= 0.246 Chirality : 0.040 0.128 892 Planarity : 0.004 0.069 945 Dihedral : 3.486 17.172 743 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.70 % Allowed : 11.85 % Favored : 87.46 % 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: 1.78 (0.34), residues: 662 helix: 2.52 (0.29), residues: 312 sheet: -1.57 (0.56), residues: 76 loop : 0.55 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS E 56 PHE 0.009 0.001 PHE d 150 TYR 0.007 0.002 TYR B 18 ARG 0.009 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 206) hydrogen bonds : angle 3.46011 ( 591) covalent geometry : bond 0.00401 ( 5340) covalent geometry : angle 0.47497 ( 7215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7958 (t0) cc_final: 0.7565 (t0) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 2.4450 time to fit residues: 134.8783 Evaluate side-chains 51 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.101408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073731 restraints weight = 32247.728| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.01 r_work: 0.3070 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5340 Z= 0.140 Angle : 0.458 5.103 7215 Z= 0.236 Chirality : 0.040 0.129 892 Planarity : 0.004 0.074 945 Dihedral : 3.434 17.056 743 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.87 % Allowed : 12.37 % Favored : 86.76 % 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: 1.83 (0.34), residues: 662 helix: 2.59 (0.29), residues: 312 sheet: -1.59 (0.56), residues: 76 loop : 0.55 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS E 56 PHE 0.008 0.001 PHE d 150 TYR 0.007 0.001 TYR B 18 ARG 0.011 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 206) hydrogen bonds : angle 3.36504 ( 591) covalent geometry : bond 0.00313 ( 5340) covalent geometry : angle 0.45839 ( 7215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7956 (t0) cc_final: 0.7549 (t0) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 2.2801 time to fit residues: 125.6250 Evaluate side-chains 55 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.100657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073073 restraints weight = 32776.656| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.00 r_work: 0.3058 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5340 Z= 0.180 Angle : 0.473 5.151 7215 Z= 0.245 Chirality : 0.040 0.128 892 Planarity : 0.004 0.081 945 Dihedral : 3.502 17.218 743 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 12.54 % Favored : 86.41 % 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: 1.80 (0.34), residues: 662 helix: 2.58 (0.29), residues: 312 sheet: -1.58 (0.56), residues: 76 loop : 0.51 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.009 0.001 PHE d 150 TYR 0.007 0.001 TYR B 18 ARG 0.012 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 206) hydrogen bonds : angle 3.42302 ( 591) covalent geometry : bond 0.00397 ( 5340) covalent geometry : angle 0.47281 ( 7215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7971 (t0) cc_final: 0.7501 (t0) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 2.0406 time to fit residues: 119.0305 Evaluate side-chains 54 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 0.0070 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.100789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073043 restraints weight = 32259.426| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.01 r_work: 0.3058 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5340 Z= 0.179 Angle : 0.481 5.915 7215 Z= 0.249 Chirality : 0.040 0.129 892 Planarity : 0.004 0.082 945 Dihedral : 3.516 17.163 743 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 13.41 % Favored : 85.54 % 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: 1.79 (0.35), residues: 662 helix: 2.58 (0.29), residues: 312 sheet: -1.60 (0.56), residues: 76 loop : 0.51 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.008 0.001 PHE d 150 TYR 0.006 0.001 TYR d 316 ARG 0.010 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 206) hydrogen bonds : angle 3.41435 ( 591) covalent geometry : bond 0.00397 ( 5340) covalent geometry : angle 0.48093 ( 7215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7960 (t0) cc_final: 0.7524 (t0) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 2.1190 time to fit residues: 114.6332 Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 22 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.101164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073351 restraints weight = 32586.313| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.04 r_work: 0.3067 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5340 Z= 0.155 Angle : 0.470 5.608 7215 Z= 0.242 Chirality : 0.040 0.127 892 Planarity : 0.004 0.082 945 Dihedral : 3.464 17.041 743 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.87 % Allowed : 13.76 % Favored : 85.37 % 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: 1.85 (0.35), residues: 662 helix: 2.64 (0.29), residues: 312 sheet: -1.62 (0.56), residues: 76 loop : 0.53 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.008 0.001 PHE d 150 TYR 0.007 0.001 TYR B 18 ARG 0.010 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 206) hydrogen bonds : angle 3.36458 ( 591) covalent geometry : bond 0.00345 ( 5340) covalent geometry : angle 0.46954 ( 7215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7954 (t0) cc_final: 0.7532 (t0) outliers start: 5 outliers final: 5 residues processed: 50 average time/residue: 2.1139 time to fit residues: 111.9138 Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.101343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073461 restraints weight = 32311.652| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.03 r_work: 0.3066 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5340 Z= 0.139 Angle : 0.465 5.621 7215 Z= 0.239 Chirality : 0.040 0.128 892 Planarity : 0.004 0.080 945 Dihedral : 3.420 16.844 743 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.70 % Allowed : 14.29 % Favored : 85.02 % 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: 1.89 (0.35), residues: 662 helix: 2.68 (0.29), residues: 312 sheet: -1.56 (0.57), residues: 76 loop : 0.53 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.008 0.001 PHE d 150 TYR 0.006 0.001 TYR d 316 ARG 0.010 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 206) hydrogen bonds : angle 3.32201 ( 591) covalent geometry : bond 0.00310 ( 5340) covalent geometry : angle 0.46464 ( 7215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7908 (t0) cc_final: 0.7435 (t0) outliers start: 4 outliers final: 5 residues processed: 52 average time/residue: 2.0943 time to fit residues: 115.3732 Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 30 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 overall best weight: 0.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN b 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.102434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074504 restraints weight = 32392.381| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.08 r_work: 0.3086 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5340 Z= 0.095 Angle : 0.454 6.721 7215 Z= 0.232 Chirality : 0.040 0.129 892 Planarity : 0.004 0.078 945 Dihedral : 3.250 16.086 743 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.35 % Allowed : 14.63 % Favored : 85.02 % 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: 2.05 (0.35), residues: 662 helix: 2.80 (0.30), residues: 312 sheet: -1.51 (0.58), residues: 76 loop : 0.63 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP d 261 HIS 0.002 0.000 HIS E 56 PHE 0.007 0.001 PHE d 150 TYR 0.004 0.001 TYR d 316 ARG 0.010 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 206) hydrogen bonds : angle 3.17280 ( 591) covalent geometry : bond 0.00217 ( 5340) covalent geometry : angle 0.45352 ( 7215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9172.39 seconds wall clock time: 161 minutes 39.85 seconds (9699.85 seconds total)