Starting phenix.real_space_refine on Wed Jul 1 23:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ft7_50741/07_2026/9ft7_50741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ft7_50741/07_2026/9ft7_50741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ft7_50741/07_2026/9ft7_50741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ft7_50741/07_2026/9ft7_50741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ft7_50741/07_2026/9ft7_50741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ft7_50741/07_2026/9ft7_50741.map" } resolution = 3.16 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= 0.001 sd= 0.043 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 K 2 8.98 5 S 22 5.16 5 C 2656 2.51 5 N 652 2.21 5 O 684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1987 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1987 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'EIC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'EIC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.09, per 1000 atoms: 0.27 Number of scatterers: 4016 At special positions: 0 Unit cell: (80.704, 69.056, 93.184, 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) K 2 19.00 S 22 16.00 O 684 8.00 N 652 7.00 C 2656 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: 0.35 Conformation dependent library (CDL) restraints added in 141.9 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 14 through 64 removed outlier: 3.746A pdb=" N ALA A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 164 removed outlier: 3.519A pdb=" N ILE A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 294 Processing helix chain 'B' and resid 15 through 64 removed outlier: 3.746A pdb=" N ALA B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 164 removed outlier: 3.519A pdb=" N ILE B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 221 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 294 347 hydrogen bonds defined for protein. 1041 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: 0.53 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1234 1.34 - 1.46: 709 1.46 - 1.57: 2137 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 4110 Sorted by residual: bond pdb=" CB THR A 116 " pdb=" CG2 THR A 116 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" CB THR B 116 " pdb=" CG2 THR B 116 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" CB THR B 138 " pdb=" CG2 THR B 138 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR A 138 " pdb=" CG2 THR A 138 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" C1 EIC B 401 " pdb=" C2 EIC B 401 " ideal model delta sigma weight residual 1.539 1.516 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 4105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 4990 1.01 - 2.02: 480 2.02 - 3.02: 78 3.02 - 4.03: 22 4.03 - 5.04: 2 Bond angle restraints: 5572 Sorted by residual: angle pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" C GLU B 42 " ideal model delta sigma weight residual 112.54 115.62 -3.08 1.51e+00 4.39e-01 4.15e+00 angle pdb=" N GLU A 42 " pdb=" CA GLU A 42 " pdb=" C GLU A 42 " ideal model delta sigma weight residual 112.54 115.62 -3.08 1.51e+00 4.39e-01 4.15e+00 angle pdb=" C PHE A 142 " pdb=" N ASN A 143 " pdb=" CA ASN A 143 " ideal model delta sigma weight residual 120.68 117.29 3.39 1.70e+00 3.46e-01 3.97e+00 angle pdb=" C PHE B 142 " pdb=" N ASN B 143 " pdb=" CA ASN B 143 " ideal model delta sigma weight residual 120.68 117.31 3.37 1.70e+00 3.46e-01 3.92e+00 angle pdb=" N THR A 138 " pdb=" CA THR A 138 " pdb=" C THR A 138 " ideal model delta sigma weight residual 111.36 113.48 -2.12 1.09e+00 8.42e-01 3.80e+00 ... (remaining 5567 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.36: 2182 16.36 - 32.72: 128 32.72 - 49.08: 24 49.08 - 65.44: 6 65.44 - 81.80: 2 Dihedral angle restraints: 2342 sinusoidal: 844 harmonic: 1498 Sorted by residual: dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA TRP B 95 " pdb=" C TRP B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLU B 42 " pdb=" C GLU B 42 " pdb=" N LEU B 43 " pdb=" CA LEU B 43 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 2339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 323 0.032 - 0.064: 231 0.064 - 0.096: 64 0.096 - 0.128: 14 0.128 - 0.160: 6 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA THR A 217 " pdb=" N THR A 217 " pdb=" C THR A 217 " pdb=" CB THR A 217 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA THR B 217 " pdb=" N THR B 217 " pdb=" C THR B 217 " pdb=" CB THR B 217 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 635 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 139 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C ILE A 139 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 139 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 140 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 139 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C ILE B 139 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE B 139 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 140 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 270 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C CYS B 270 " 0.039 2.00e-02 2.50e+03 pdb=" O CYS B 270 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS B 271 " -0.013 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.88: 1539 2.88 - 3.45: 4651 3.45 - 4.01: 7541 4.01 - 4.58: 11069 4.58 - 5.14: 15538 Nonbonded interactions: 40338 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OE2 GLU B 79 " model vdw 2.317 3.040 nonbonded pdb=" OE2 GLU A 79 " pdb=" OH TYR B 78 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR A 216 " pdb=" OD1 ASN A 261 " model vdw 2.371 3.040 nonbonded pdb=" OH TYR B 216 " pdb=" OD1 ASN B 261 " model vdw 2.371 3.040 nonbonded pdb=" NH1 ARG A 94 " pdb=" OE1 GLN A 247 " model vdw 2.384 3.120 ... (remaining 40333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 401) selection = chain 'B' } 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: 0.970 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.290 Find NCS groups from input model: 0.070 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 0.040 4110 Z= 0.261 Angle : 0.666 5.041 5572 Z= 0.415 Chirality : 0.045 0.160 638 Planarity : 0.006 0.029 690 Dihedral : 11.556 81.805 1382 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.52 (0.34), residues: 508 helix: 1.31 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.10 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 87 TYR 0.019 0.004 TYR B 251 PHE 0.020 0.002 PHE B 38 TRP 0.029 0.004 TRP A 53 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.26 ( 4110) covalent geometry : angle 0.66575 / 0.42 ( 5572) hydrogen bonds : bond 0.12492 / 8.49 ( 347) hydrogen bonds : angle 5.03666 / 3.83 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.136 Fit side-chains REVERT: A 198 MET cc_start: 0.7665 (ttp) cc_final: 0.7320 (ttt) REVERT: B 198 MET cc_start: 0.7675 (ttp) cc_final: 0.7329 (ttt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0614 time to fit residues: 2.4555 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117446 restraints weight = 4283.453| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.37 r_work: 0.3229 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4110 Z= 0.147 Angle : 0.469 5.722 5572 Z= 0.263 Chirality : 0.035 0.154 638 Planarity : 0.003 0.025 690 Dihedral : 6.749 56.793 592 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.51 % Allowed : 3.54 % Favored : 95.96 % 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: 4.28 (0.35), residues: 508 helix: 3.17 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.05 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.010 0.001 TYR B 251 PHE 0.008 0.001 PHE A 232 TRP 0.010 0.001 TRP B 53 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4110) covalent geometry : angle 0.46852 / 0.26 ( 5572) hydrogen bonds : bond 0.04633 / 3.18 ( 347) hydrogen bonds : angle 3.21265 / 2.46 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.090 Fit side-chains REVERT: A 80 GLU cc_start: 0.6909 (tt0) cc_final: 0.6591 (mt-10) REVERT: A 198 MET cc_start: 0.6879 (ttp) cc_final: 0.6536 (ttt) REVERT: B 80 GLU cc_start: 0.6893 (tt0) cc_final: 0.6573 (mt-10) REVERT: B 198 MET cc_start: 0.6898 (ttp) cc_final: 0.6557 (ttt) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0358 time to fit residues: 1.3661 Evaluate side-chains 20 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.0170 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 250 HIS B 247 GLN B 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118101 restraints weight = 4234.217| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.36 r_work: 0.3247 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4110 Z= 0.132 Angle : 0.430 5.216 5572 Z= 0.238 Chirality : 0.034 0.154 638 Planarity : 0.003 0.027 690 Dihedral : 6.669 57.401 592 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.52 % Allowed : 3.03 % Favored : 95.45 % 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: 4.93 (0.36), residues: 508 helix: 3.55 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.62 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 94 TYR 0.009 0.001 TYR B 229 PHE 0.008 0.001 PHE A 232 TRP 0.005 0.001 TRP A 53 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4110) covalent geometry : angle 0.42956 / 0.24 ( 5572) hydrogen bonds : bond 0.04289 / 2.95 ( 347) hydrogen bonds : angle 2.98252 / 2.28 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.136 Fit side-chains REVERT: A 80 GLU cc_start: 0.6827 (tt0) cc_final: 0.6562 (mt-10) REVERT: A 198 MET cc_start: 0.6881 (ttp) cc_final: 0.6544 (ttt) REVERT: B 80 GLU cc_start: 0.6817 (tt0) cc_final: 0.6553 (mt-10) REVERT: B 198 MET cc_start: 0.6895 (ttp) cc_final: 0.6559 (ttt) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.0426 time to fit residues: 1.8674 Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.0040 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.0040 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 250 HIS B 247 GLN B 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121876 restraints weight = 4168.317| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.35 r_work: 0.3293 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4110 Z= 0.103 Angle : 0.381 4.917 5572 Z= 0.213 Chirality : 0.033 0.135 638 Planarity : 0.002 0.028 690 Dihedral : 6.529 57.354 592 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.01 % Allowed : 5.30 % Favored : 93.69 % 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: 5.16 (0.36), residues: 508 helix: 3.74 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.54 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.008 0.001 TYR A 229 PHE 0.006 0.001 PHE A 230 TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 4110) covalent geometry : angle 0.38116 / 0.21 ( 5572) hydrogen bonds : bond 0.03776 / 2.60 ( 347) hydrogen bonds : angle 2.80245 / 2.13 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.150 Fit side-chains REVERT: A 80 GLU cc_start: 0.6881 (tt0) cc_final: 0.6579 (mt-10) REVERT: A 198 MET cc_start: 0.6909 (ttp) cc_final: 0.6560 (ttt) REVERT: B 80 GLU cc_start: 0.6867 (tt0) cc_final: 0.6568 (mt-10) REVERT: B 198 MET cc_start: 0.6918 (ttp) cc_final: 0.6571 (ttt) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.0468 time to fit residues: 1.9138 Evaluate side-chains 26 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117318 restraints weight = 4246.109| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.36 r_work: 0.3239 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4110 Z= 0.142 Angle : 0.420 4.948 5572 Z= 0.233 Chirality : 0.034 0.153 638 Planarity : 0.003 0.026 690 Dihedral : 6.670 57.303 592 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.02 % Allowed : 4.04 % Favored : 93.94 % 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: 5.06 (0.36), residues: 508 helix: 3.69 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.39 (0.73), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.009 0.001 TYR A 229 PHE 0.009 0.001 PHE B 232 TRP 0.003 0.001 TRP A 53 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 4110) covalent geometry : angle 0.41995 / 0.23 ( 5572) hydrogen bonds : bond 0.04229 / 2.91 ( 347) hydrogen bonds : angle 2.91472 / 2.22 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.086 Fit side-chains REVERT: A 80 GLU cc_start: 0.6867 (tt0) cc_final: 0.6563 (mt-10) REVERT: A 198 MET cc_start: 0.6963 (ttp) cc_final: 0.6636 (ttt) REVERT: B 80 GLU cc_start: 0.6847 (tt0) cc_final: 0.6547 (mt-10) REVERT: B 198 MET cc_start: 0.6971 (ttp) cc_final: 0.6642 (ttt) outliers start: 8 outliers final: 6 residues processed: 26 average time/residue: 0.0636 time to fit residues: 2.1786 Evaluate side-chains 26 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119435 restraints weight = 4276.447| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.38 r_work: 0.3260 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4110 Z= 0.116 Angle : 0.391 4.884 5572 Z= 0.217 Chirality : 0.033 0.144 638 Planarity : 0.002 0.027 690 Dihedral : 6.613 57.146 592 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.53 % Allowed : 4.55 % Favored : 92.93 % 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: 5.12 (0.36), residues: 508 helix: 3.74 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.35 (0.72), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.008 0.001 TYR A 229 PHE 0.007 0.001 PHE B 232 TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4110) covalent geometry : angle 0.39064 / 0.22 ( 5572) hydrogen bonds : bond 0.03917 / 2.70 ( 347) hydrogen bonds : angle 2.80924 / 2.13 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.091 Fit side-chains REVERT: A 80 GLU cc_start: 0.6851 (tt0) cc_final: 0.6550 (mt-10) REVERT: A 198 MET cc_start: 0.6925 (ttp) cc_final: 0.6595 (ttt) REVERT: B 80 GLU cc_start: 0.6851 (tt0) cc_final: 0.6551 (mt-10) REVERT: B 198 MET cc_start: 0.6953 (ttp) cc_final: 0.6622 (ttt) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.0691 time to fit residues: 2.8860 Evaluate side-chains 34 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118101 restraints weight = 4284.621| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.38 r_work: 0.3243 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4110 Z= 0.127 Angle : 0.402 4.876 5572 Z= 0.223 Chirality : 0.033 0.149 638 Planarity : 0.002 0.026 690 Dihedral : 6.660 57.198 592 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.53 % Allowed : 4.04 % Favored : 93.43 % 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: 5.14 (0.36), residues: 508 helix: 3.76 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.36 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 94 TYR 0.009 0.001 TYR B 229 PHE 0.008 0.001 PHE B 232 TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 4110) covalent geometry : angle 0.40214 / 0.22 ( 5572) hydrogen bonds : bond 0.04033 / 2.77 ( 347) hydrogen bonds : angle 2.83528 / 2.15 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.159 Fit side-chains REVERT: A 80 GLU cc_start: 0.6838 (tt0) cc_final: 0.6511 (mt-10) REVERT: A 198 MET cc_start: 0.6928 (ttp) cc_final: 0.6605 (ttt) REVERT: B 80 GLU cc_start: 0.6825 (tt0) cc_final: 0.6501 (mt-10) REVERT: B 198 MET cc_start: 0.6962 (ttp) cc_final: 0.6638 (ttt) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.0652 time to fit residues: 2.5848 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.158173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117379 restraints weight = 4255.793| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.35 r_work: 0.3237 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4110 Z= 0.135 Angle : 0.409 4.882 5572 Z= 0.227 Chirality : 0.034 0.152 638 Planarity : 0.002 0.025 690 Dihedral : 6.720 56.968 592 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.53 % Allowed : 4.04 % Favored : 93.43 % 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: 5.10 (0.36), residues: 508 helix: 3.75 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.24 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 62 TYR 0.009 0.001 TYR B 229 PHE 0.008 0.001 PHE A 232 TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4110) covalent geometry : angle 0.40934 / 0.23 ( 5572) hydrogen bonds : bond 0.04140 / 2.85 ( 347) hydrogen bonds : angle 2.86429 / 2.17 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.146 Fit side-chains REVERT: A 80 GLU cc_start: 0.6870 (tt0) cc_final: 0.6544 (mt-10) REVERT: B 80 GLU cc_start: 0.6863 (tt0) cc_final: 0.6539 (mt-10) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.0704 time to fit residues: 2.8297 Evaluate side-chains 29 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 46 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118801 restraints weight = 4280.535| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.36 r_work: 0.3257 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4110 Z= 0.116 Angle : 0.386 4.833 5572 Z= 0.215 Chirality : 0.033 0.144 638 Planarity : 0.002 0.025 690 Dihedral : 6.652 57.074 592 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.02 % Allowed : 5.56 % Favored : 92.42 % 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: 5.15 (0.36), residues: 508 helix: 3.78 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.29 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.008 0.001 TYR B 229 PHE 0.007 0.001 PHE B 232 TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 4110) covalent geometry : angle 0.38554 / 0.21 ( 5572) hydrogen bonds : bond 0.03905 / 2.68 ( 347) hydrogen bonds : angle 2.78608 / 2.11 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.168 Fit side-chains REVERT: A 80 GLU cc_start: 0.6851 (tt0) cc_final: 0.6509 (mt-10) REVERT: B 80 GLU cc_start: 0.6842 (tt0) cc_final: 0.6506 (mt-10) outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.0723 time to fit residues: 2.9213 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118108 restraints weight = 4227.857| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.36 r_work: 0.3250 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4110 Z= 0.129 Angle : 0.403 4.826 5572 Z= 0.223 Chirality : 0.033 0.149 638 Planarity : 0.002 0.025 690 Dihedral : 6.677 57.046 592 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.02 % Allowed : 5.05 % Favored : 92.93 % 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: 5.13 (0.36), residues: 508 helix: 3.77 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.23 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.008 0.001 TYR B 229 PHE 0.008 0.001 PHE A 232 TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4110) covalent geometry : angle 0.40275 / 0.22 ( 5572) hydrogen bonds : bond 0.04031 / 2.77 ( 347) hydrogen bonds : angle 2.82108 / 2.14 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.142 Fit side-chains REVERT: A 80 GLU cc_start: 0.6870 (tt0) cc_final: 0.6551 (mt-10) REVERT: B 80 GLU cc_start: 0.6868 (tt0) cc_final: 0.6550 (mt-10) outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.0688 time to fit residues: 2.7322 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 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 = 0.3912 r_free = 0.3912 target = 0.160116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119021 restraints weight = 4223.103| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.36 r_work: 0.3262 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4110 Z= 0.118 Angle : 0.393 4.817 5572 Z= 0.218 Chirality : 0.033 0.144 638 Planarity : 0.002 0.025 690 Dihedral : 6.642 57.229 592 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.02 % Allowed : 4.55 % Favored : 93.43 % 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: 5.16 (0.36), residues: 508 helix: 3.79 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.26 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 62 TYR 0.008 0.001 TYR A 229 PHE 0.007 0.001 PHE A 232 TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4110) covalent geometry : angle 0.39298 / 0.22 ( 5572) hydrogen bonds : bond 0.03902 / 2.68 ( 347) hydrogen bonds : angle 2.78090 / 2.11 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 916.76 seconds wall clock time: 16 minutes 26.33 seconds (986.33 seconds total)