Starting phenix.real_space_refine on Wed Jun 3 09:43:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22rd_68616/06_2026/22rd_68616.cif Found real_map, /net/cci-nas-00/data/ceres_data/22rd_68616/06_2026/22rd_68616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22rd_68616/06_2026/22rd_68616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22rd_68616/06_2026/22rd_68616.map" model { file = "/net/cci-nas-00/data/ceres_data/22rd_68616/06_2026/22rd_68616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22rd_68616/06_2026/22rd_68616.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 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 10 5.16 5 C 1432 2.51 5 N 399 2.21 5 O 388 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2232 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2194 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 13, 'TRANS': 255} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'937': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.84, per 1000 atoms: 0.38 Number of scatterers: 2232 At special positions: 0 Unit cell: (53.6472, 58.8629, 78.2355, 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 10 16.00 F 3 9.00 O 388 8.00 N 399 7.00 C 1432 6.00 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: 0.17 Conformation dependent library (CDL) restraints added in 85.7 milliseconds 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 40.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.549A pdb=" N LEU A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 91 through 108 removed outlier: 3.717A pdb=" N ARG A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 4.090A pdb=" N LEU A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 170 removed outlier: 3.893A pdb=" N GLN A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 4.667A pdb=" N LEU A 197 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 198 " --> pdb=" O PHE A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 198' Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.905A pdb=" N VAL A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.769A pdb=" N LEU A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 62 removed outlier: 3.540A pdb=" N GLY A 118 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184 88 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.29 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 353 1.31 - 1.43: 602 1.43 - 1.56: 1315 1.56 - 1.68: 0 1.68 - 1.81: 14 Bond restraints: 2284 Sorted by residual: bond pdb=" C15 937 A 401 " pdb=" N28 937 A 401 " ideal model delta sigma weight residual 1.339 1.452 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C2 937 A 401 " pdb=" N14 937 A 401 " ideal model delta sigma weight residual 1.364 1.455 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" N11 937 A 401 " pdb=" N12 937 A 401 " ideal model delta sigma weight residual 1.314 1.401 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C7 937 A 401 " pdb=" C8 937 A 401 " ideal model delta sigma weight residual 1.531 1.445 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C17 937 A 401 " pdb=" N14 937 A 401 " ideal model delta sigma weight residual 1.390 1.454 -0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 2279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 2961 1.78 - 3.55: 85 3.55 - 5.33: 26 5.33 - 7.11: 4 7.11 - 8.89: 4 Bond angle restraints: 3080 Sorted by residual: angle pdb=" C ARG A 136 " pdb=" CA ARG A 136 " pdb=" CB ARG A 136 " ideal model delta sigma weight residual 116.63 111.42 5.21 1.16e+00 7.43e-01 2.02e+01 angle pdb=" C ASP A 122 " pdb=" CA ASP A 122 " pdb=" CB ASP A 122 " ideal model delta sigma weight residual 110.36 117.46 -7.10 1.78e+00 3.16e-01 1.59e+01 angle pdb=" C19 937 A 401 " pdb=" N32 937 A 401 " pdb=" C33 937 A 401 " ideal model delta sigma weight residual 117.91 109.02 8.89 3.00e+00 1.11e-01 8.78e+00 angle pdb=" N GLY A 227 " pdb=" CA GLY A 227 " pdb=" C GLY A 227 " ideal model delta sigma weight residual 111.36 114.57 -3.21 1.17e+00 7.31e-01 7.55e+00 angle pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta sigma weight residual 110.54 114.05 -3.51 1.36e+00 5.41e-01 6.67e+00 ... (remaining 3075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 1218 17.63 - 35.26: 125 35.26 - 52.89: 28 52.89 - 70.52: 16 70.52 - 88.15: 2 Dihedral angle restraints: 1389 sinusoidal: 606 harmonic: 783 Sorted by residual: dihedral pdb=" CA ARG A 171 " pdb=" CB ARG A 171 " pdb=" CG ARG A 171 " pdb=" CD ARG A 171 " ideal model delta sinusoidal sigma weight residual 60.00 119.35 -59.35 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU A 221 " pdb=" CB GLU A 221 " pdb=" CG GLU A 221 " pdb=" CD GLU A 221 " ideal model delta sinusoidal sigma weight residual -60.00 -116.13 56.13 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS A 226 " pdb=" CB LYS A 226 " pdb=" CG LYS A 226 " pdb=" CD LYS A 226 " ideal model delta sinusoidal sigma weight residual 180.00 -125.54 -54.46 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 1386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 185 0.029 - 0.058: 83 0.058 - 0.087: 34 0.087 - 0.116: 25 0.116 - 0.146: 4 Chirality restraints: 331 Sorted by residual: chirality pdb=" CG LEU A 108 " pdb=" CB LEU A 108 " pdb=" CD1 LEU A 108 " pdb=" CD2 LEU A 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 40 " pdb=" N ILE A 40 " pdb=" C ILE A 40 " pdb=" CB ILE A 40 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL A 54 " pdb=" N VAL A 54 " pdb=" C VAL A 54 " pdb=" CB VAL A 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 328 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 262 " 0.123 9.50e-02 1.11e+02 5.54e-02 2.32e+00 pdb=" NE ARG A 262 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 262 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 262 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 262 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 238 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C GLY A 238 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY A 238 " -0.010 2.00e-02 2.50e+03 pdb=" N CYS A 239 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 242 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C TYR A 242 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR A 242 " 0.009 2.00e-02 2.50e+03 pdb=" N THR A 243 " 0.008 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1030 2.97 - 3.45: 2099 3.45 - 3.94: 3306 3.94 - 4.42: 3914 4.42 - 4.90: 6536 Nonbonded interactions: 16885 Sorted by model distance: nonbonded pdb=" OD1 ASP A 122 " pdb=" N ASN A 123 " model vdw 2.489 3.120 nonbonded pdb=" O THR A 75 " pdb=" OG1 THR A 75 " model vdw 2.557 3.040 nonbonded pdb=" N ASP A 122 " pdb=" O ASP A 122 " model vdw 2.609 2.496 nonbonded pdb=" N GLU A 39 " pdb=" OE1 GLU A 39 " model vdw 2.632 3.120 nonbonded pdb=" N32 937 A 401 " pdb=" N35 937 A 401 " model vdw 2.637 2.560 ... (remaining 16880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 4.270 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.006 0.113 2284 Z= 0.309 Angle : 0.839 8.887 3080 Z= 0.433 Chirality : 0.046 0.146 331 Planarity : 0.006 0.055 390 Dihedral : 16.378 88.152 883 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.65 % Allowed : 16.94 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.48), residues: 267 helix: 0.36 (0.54), residues: 87 sheet: 0.40 (0.92), residues: 36 loop : -0.93 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 262 TYR 0.008 0.001 TYR A 155 PHE 0.011 0.001 PHE A 183 TRP 0.008 0.002 TRP A 235 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.31 ( 2284) covalent geometry : angle 0.83900 / 0.43 ( 3080) hydrogen bonds : bond 0.13197 / 8.35 ( 88) hydrogen bonds : angle 6.74219 / 4.61 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.098 Fit side-chains REVERT: A 194 ASP cc_start: 0.8632 (t70) cc_final: 0.8276 (t0) REVERT: A 209 LYS cc_start: 0.7747 (mttt) cc_final: 0.7112 (ptmt) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0508 time to fit residues: 1.9068 Evaluate side-chains 29 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 287 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.174645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.165905 restraints weight = 3152.647| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.30 r_work: 0.3937 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2284 Z= 0.149 Angle : 0.600 4.852 3080 Z= 0.315 Chirality : 0.046 0.128 331 Planarity : 0.005 0.029 390 Dihedral : 10.661 85.139 323 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.31 % Allowed : 16.53 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.48), residues: 267 helix: 1.04 (0.57), residues: 88 sheet: -0.18 (0.86), residues: 36 loop : -1.18 (0.45), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 262 TYR 0.007 0.001 TYR A 155 PHE 0.012 0.002 PHE A 120 TRP 0.009 0.002 TRP A 235 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 2284) covalent geometry : angle 0.60008 / 0.31 ( 3080) hydrogen bonds : bond 0.05454 / 3.61 ( 88) hydrogen bonds : angle 5.00849 / 3.40 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.089 Fit side-chains REVERT: A 194 ASP cc_start: 0.8606 (t70) cc_final: 0.8174 (t0) REVERT: A 209 LYS cc_start: 0.7766 (mttt) cc_final: 0.6988 (ptmt) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.0599 time to fit residues: 2.3563 Evaluate side-chains 29 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.170190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162620 restraints weight = 3147.729| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.08 r_work: 0.3940 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2284 Z= 0.134 Angle : 0.559 4.799 3080 Z= 0.292 Chirality : 0.045 0.125 331 Planarity : 0.004 0.025 390 Dihedral : 10.180 85.376 320 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.72 % Allowed : 16.94 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.49), residues: 267 helix: 1.11 (0.58), residues: 89 sheet: -0.40 (0.87), residues: 36 loop : -1.22 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 48 TYR 0.009 0.001 TYR A 155 PHE 0.011 0.001 PHE A 120 TRP 0.011 0.003 TRP A 235 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 2284) covalent geometry : angle 0.55875 / 0.29 ( 3080) hydrogen bonds : bond 0.04948 / 3.27 ( 88) hydrogen bonds : angle 4.65456 / 3.16 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.056 Fit side-chains REVERT: A 194 ASP cc_start: 0.8557 (t70) cc_final: 0.8189 (t0) REVERT: A 209 LYS cc_start: 0.7736 (mttt) cc_final: 0.7040 (ptmt) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.0400 time to fit residues: 1.5672 Evaluate side-chains 27 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.0050 chunk 5 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.4692 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.170508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163088 restraints weight = 3062.102| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.03 r_work: 0.3954 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2284 Z= 0.121 Angle : 0.543 4.755 3080 Z= 0.284 Chirality : 0.044 0.128 331 Planarity : 0.004 0.047 390 Dihedral : 10.102 85.349 320 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.55 % Allowed : 15.70 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.49), residues: 267 helix: 1.11 (0.58), residues: 89 sheet: -0.48 (0.88), residues: 36 loop : -1.20 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 175 TYR 0.009 0.001 TYR A 155 PHE 0.011 0.001 PHE A 120 TRP 0.016 0.003 TRP A 235 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 2284) covalent geometry : angle 0.54266 / 0.28 ( 3080) hydrogen bonds : bond 0.04714 / 3.14 ( 88) hydrogen bonds : angle 4.49821 / 3.10 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.090 Fit side-chains REVERT: A 194 ASP cc_start: 0.8562 (t70) cc_final: 0.8196 (t0) REVERT: A 209 LYS cc_start: 0.7661 (mttt) cc_final: 0.7006 (ptmt) outliers start: 11 outliers final: 9 residues processed: 32 average time/residue: 0.0466 time to fit residues: 1.9205 Evaluate side-chains 29 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161575 restraints weight = 3101.351| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.06 r_work: 0.3928 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2284 Z= 0.141 Angle : 0.563 4.878 3080 Z= 0.296 Chirality : 0.045 0.124 331 Planarity : 0.004 0.024 390 Dihedral : 10.224 85.728 320 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.55 % Allowed : 17.36 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.49), residues: 267 helix: 0.96 (0.57), residues: 89 sheet: -0.52 (0.89), residues: 36 loop : -1.26 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.010 0.001 TYR A 155 PHE 0.011 0.001 PHE A 120 TRP 0.016 0.004 TRP A 235 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 2284) covalent geometry : angle 0.56334 / 0.30 ( 3080) hydrogen bonds : bond 0.04974 / 3.34 ( 88) hydrogen bonds : angle 4.53058 / 3.15 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.068 Fit side-chains REVERT: A 194 ASP cc_start: 0.8575 (t70) cc_final: 0.8215 (t0) REVERT: A 209 LYS cc_start: 0.7691 (mttt) cc_final: 0.7007 (ptmt) outliers start: 11 outliers final: 10 residues processed: 31 average time/residue: 0.0370 time to fit residues: 1.5293 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 0 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.169140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161634 restraints weight = 3058.110| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.04 r_work: 0.3932 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.003 0.019 2284 Z= 0.136 Angle : 0.554 4.880 3080 Z= 0.289 Chirality : 0.045 0.138 331 Planarity : 0.004 0.025 390 Dihedral : 10.247 85.818 320 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.55 % Allowed : 16.94 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.49), residues: 267 helix: 1.00 (0.58), residues: 89 sheet: -0.55 (0.89), residues: 36 loop : -1.25 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.010 0.001 TYR A 155 PHE 0.011 0.001 PHE A 120 TRP 0.014 0.003 TRP A 235 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 2284) covalent geometry : angle 0.55427 / 0.29 ( 3080) hydrogen bonds : bond 0.04875 / 3.26 ( 88) hydrogen bonds : angle 4.42432 / 3.07 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.127 Fit side-chains REVERT: A 194 ASP cc_start: 0.8542 (t70) cc_final: 0.8201 (t0) REVERT: A 209 LYS cc_start: 0.7696 (mttt) cc_final: 0.7017 (ptmt) outliers start: 11 outliers final: 10 residues processed: 31 average time/residue: 0.0401 time to fit residues: 1.6808 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 0.0370 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.171402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163737 restraints weight = 3036.443| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.06 r_work: 0.3952 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2284 Z= 0.104 Angle : 0.518 5.334 3080 Z= 0.269 Chirality : 0.044 0.135 331 Planarity : 0.003 0.025 390 Dihedral : 10.045 85.667 320 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.13 % Allowed : 18.18 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.50), residues: 267 helix: 1.26 (0.58), residues: 89 sheet: -0.44 (0.90), residues: 36 loop : -1.07 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.009 0.001 TYR A 155 PHE 0.010 0.001 PHE A 120 TRP 0.011 0.002 TRP A 235 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 2284) covalent geometry : angle 0.51766 / 0.27 ( 3080) hydrogen bonds : bond 0.04165 / 2.76 ( 88) hydrogen bonds : angle 4.21135 / 2.94 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.054 Fit side-chains REVERT: A 194 ASP cc_start: 0.8529 (t70) cc_final: 0.8173 (t0) REVERT: A 209 LYS cc_start: 0.7632 (mttt) cc_final: 0.6941 (ptmt) outliers start: 10 outliers final: 9 residues processed: 32 average time/residue: 0.0437 time to fit residues: 1.7767 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.170100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162447 restraints weight = 3083.282| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.08 r_work: 0.3937 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2284 Z= 0.126 Angle : 0.548 4.991 3080 Z= 0.285 Chirality : 0.044 0.141 331 Planarity : 0.005 0.064 390 Dihedral : 10.176 85.938 320 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.13 % Allowed : 17.77 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.50), residues: 267 helix: 1.01 (0.57), residues: 89 sheet: -0.42 (0.90), residues: 36 loop : -1.12 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.010 0.001 TYR A 155 PHE 0.015 0.001 PHE A 251 TRP 0.013 0.003 TRP A 235 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 2284) covalent geometry : angle 0.54835 / 0.29 ( 3080) hydrogen bonds : bond 0.04526 / 3.00 ( 88) hydrogen bonds : angle 4.34754 / 2.96 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.054 Fit side-chains REVERT: A 194 ASP cc_start: 0.8536 (t70) cc_final: 0.8176 (t0) REVERT: A 209 LYS cc_start: 0.7652 (mttt) cc_final: 0.6980 (ptmt) outliers start: 10 outliers final: 10 residues processed: 31 average time/residue: 0.0434 time to fit residues: 1.6864 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.0070 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.170549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162783 restraints weight = 3137.087| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.10 r_work: 0.3940 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2284 Z= 0.114 Angle : 0.535 5.012 3080 Z= 0.279 Chirality : 0.044 0.140 331 Planarity : 0.004 0.051 390 Dihedral : 10.154 85.957 320 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.55 % Allowed : 18.18 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.50), residues: 267 helix: 1.11 (0.58), residues: 89 sheet: -0.41 (0.91), residues: 36 loop : -1.04 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.009 0.001 TYR A 155 PHE 0.010 0.001 PHE A 120 TRP 0.011 0.003 TRP A 235 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 2284) covalent geometry : angle 0.53522 / 0.28 ( 3080) hydrogen bonds : bond 0.04330 / 2.86 ( 88) hydrogen bonds : angle 4.33111 / 2.94 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.070 Fit side-chains REVERT: A 194 ASP cc_start: 0.8544 (t70) cc_final: 0.8186 (t0) REVERT: A 209 LYS cc_start: 0.7630 (mttt) cc_final: 0.6914 (ptmt) outliers start: 11 outliers final: 10 residues processed: 32 average time/residue: 0.0247 time to fit residues: 1.0650 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 23 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.174597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.166874 restraints weight = 3039.901| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.06 r_work: 0.3990 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2284 Z= 0.103 Angle : 0.529 5.470 3080 Z= 0.276 Chirality : 0.043 0.144 331 Planarity : 0.004 0.048 390 Dihedral : 10.090 85.978 320 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.72 % Allowed : 18.60 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.51), residues: 267 helix: 1.19 (0.58), residues: 89 sheet: -0.12 (0.92), residues: 36 loop : -0.97 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.008 0.001 TYR A 155 PHE 0.010 0.001 PHE A 120 TRP 0.010 0.002 TRP A 235 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 2284) covalent geometry : angle 0.52944 / 0.28 ( 3080) hydrogen bonds : bond 0.04124 / 2.71 ( 88) hydrogen bonds : angle 4.26641 / 2.90 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.055 Fit side-chains REVERT: A 194 ASP cc_start: 0.8526 (t70) cc_final: 0.8180 (t0) REVERT: A 209 LYS cc_start: 0.7638 (mttt) cc_final: 0.6917 (ptmt) REVERT: A 284 LYS cc_start: 0.7791 (mttt) cc_final: 0.7185 (mmtt) outliers start: 9 outliers final: 9 residues processed: 32 average time/residue: 0.0387 time to fit residues: 1.5692 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 301 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.174583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166776 restraints weight = 3055.008| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.08 r_work: 0.3991 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2284 Z= 0.104 Angle : 0.527 5.647 3080 Z= 0.273 Chirality : 0.043 0.150 331 Planarity : 0.004 0.043 390 Dihedral : 10.061 86.152 320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.13 % Allowed : 18.18 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.51), residues: 267 helix: 1.23 (0.58), residues: 89 sheet: 0.05 (0.94), residues: 36 loop : -0.95 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.008 0.001 TYR A 155 PHE 0.010 0.001 PHE A 120 TRP 0.011 0.002 TRP A 235 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 2284) covalent geometry : angle 0.52700 / 0.27 ( 3080) hydrogen bonds : bond 0.04039 / 2.65 ( 88) hydrogen bonds : angle 4.20294 / 2.86 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 744.01 seconds wall clock time: 13 minutes 22.88 seconds (802.88 seconds total)