Starting phenix.real_space_refine on Tue Feb 3 14:40:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ft7_50741/02_2026/9ft7_50741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ft7_50741/02_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_50741/02_2026/9ft7_50741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ft7_50741/02_2026/9ft7_50741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ft7_50741/02_2026/9ft7_50741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ft7_50741/02_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-2.0-5952/lib/python3.9/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, 22 Unusual residues: {' K': 2, 'EIC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 1.06, per 1000 atoms: 0.26 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: 0.36 Conformation dependent library (CDL) restraints added in 165.1 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: 0.11 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: 0.66 Time building geometry restraints manager: 0.48 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.130 Find NCS groups from input model: 0.080 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 covalent geometry : bond 0.00633 ( 4110) covalent geometry : angle 0.66575 ( 5572) hydrogen bonds : bond 0.12492 ( 347) hydrogen bonds : angle 5.03666 ( 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 : 0.154 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: 0.0807 time to fit residues: 3.1489 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 : 0.143 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3933 r_free = 0.3933 target = 0.159043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119476 restraints weight = 4353.053| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.29 r_work: 0.3286 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1160 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= 0.146 Angle : 0.463 5.739 5572 Z= 0.261 Chirality : 0.035 0.154 638 Planarity : 0.003 0.024 690 Dihedral : 6.733 55.552 592 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 4.16 (0.35), residues: 508 helix: 3.16 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.51 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.011 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 covalent geometry : bond 0.00340 ( 4110) covalent geometry : angle 0.46262 ( 5572) hydrogen bonds : bond 0.04673 ( 347) hydrogen bonds : angle 3.21369 ( 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 25 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.160 Fit side-chains REVERT: A 80 GLU cc_start: 0.7074 (tt0) cc_final: 0.6717 (mt-10) REVERT: A 198 MET cc_start: 0.7029 (ttp) cc_final: 0.6685 (ttt) REVERT: B 80 GLU cc_start: 0.7076 (tt0) cc_final: 0.6731 (mt-10) REVERT: B 198 MET cc_start: 0.7042 (ttp) cc_final: 0.6699 (ttt) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.0682 time to fit residues: 2.3774 Evaluate side-chains 21 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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: 0.7980 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3879 r_free = 0.3879 target = 0.157246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116688 restraints weight = 4231.764| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.35 r_work: 0.3230 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4110 Z= 0.148 Angle : 0.444 5.288 5572 Z= 0.246 Chirality : 0.035 0.158 638 Planarity : 0.003 0.026 690 Dihedral : 6.764 56.427 592 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.52 % Allowed : 4.29 % Favored : 94.19 % 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: 4.71 (0.36), residues: 508 helix: 3.52 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.87 (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 A 229 PHE 0.008 0.001 PHE B 232 TRP 0.005 0.001 TRP A 53 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4110) covalent geometry : angle 0.44422 ( 5572) hydrogen bonds : bond 0.04483 ( 347) hydrogen bonds : angle 3.03935 ( 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 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.147 Fit side-chains REVERT: A 80 GLU cc_start: 0.6863 (tt0) cc_final: 0.6583 (mt-10) REVERT: A 198 MET cc_start: 0.6912 (ttp) cc_final: 0.6579 (ttt) REVERT: B 80 GLU cc_start: 0.6851 (tt0) cc_final: 0.6574 (mt-10) REVERT: B 198 MET cc_start: 0.6919 (ttp) cc_final: 0.6587 (ttt) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.0787 time to fit residues: 2.8881 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 : 0.140 ------------------------------------------------------------------------------- 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: 5.9990 chunk 44 optimal weight: 0.9990 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: 0.7980 chunk 43 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 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 250 HIS B 247 GLN B 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118110 restraints weight = 4170.769| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.34 r_work: 0.3248 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4110 Z= 0.125 Angle : 0.405 4.885 5572 Z= 0.227 Chirality : 0.034 0.144 638 Planarity : 0.003 0.027 690 Dihedral : 6.681 55.644 592 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.52 % Allowed : 5.05 % 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: 4.90 (0.36), residues: 508 helix: 3.65 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.88 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.009 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 A 64 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4110) covalent geometry : angle 0.40457 ( 5572) hydrogen bonds : bond 0.04112 ( 347) hydrogen bonds : angle 2.87777 ( 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: 6 poor density : 22 time to evaluate : 0.142 Fit side-chains REVERT: A 80 GLU cc_start: 0.6840 (tt0) cc_final: 0.6550 (mt-10) REVERT: A 198 MET cc_start: 0.6883 (ttp) cc_final: 0.6550 (ttt) REVERT: B 80 GLU cc_start: 0.6832 (tt0) cc_final: 0.6544 (mt-10) REVERT: B 198 MET cc_start: 0.6899 (ttp) cc_final: 0.6569 (ttt) outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.0778 time to fit residues: 2.8637 Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 247 GLN B 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116779 restraints weight = 4233.967| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.36 r_work: 0.3229 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4110 Z= 0.136 Angle : 0.413 4.909 5572 Z= 0.229 Chirality : 0.034 0.152 638 Planarity : 0.003 0.026 690 Dihedral : 6.736 56.428 592 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 4.93 (0.36), residues: 508 helix: 3.68 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.87 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 94 TYR 0.009 0.001 TYR A 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 covalent geometry : bond 0.00318 ( 4110) covalent geometry : angle 0.41288 ( 5572) hydrogen bonds : bond 0.04230 ( 347) hydrogen bonds : angle 2.89976 ( 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 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.112 Fit side-chains REVERT: A 80 GLU cc_start: 0.6870 (tt0) cc_final: 0.6564 (mt-10) REVERT: A 198 MET cc_start: 0.6919 (ttp) cc_final: 0.6591 (ttt) REVERT: B 80 GLU cc_start: 0.6850 (tt0) cc_final: 0.6549 (mt-10) REVERT: B 198 MET cc_start: 0.6934 (ttp) cc_final: 0.6604 (ttt) outliers start: 10 outliers final: 8 residues processed: 28 average time/residue: 0.0536 time to fit residues: 2.0776 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 : 0.135 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118332 restraints weight = 4271.532| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.38 r_work: 0.3257 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1802 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= 0.119 Angle : 0.389 4.900 5572 Z= 0.217 Chirality : 0.033 0.146 638 Planarity : 0.002 0.026 690 Dihedral : 6.682 56.288 592 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.53 % Allowed : 4.29 % Favored : 93.18 % 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: 4.99 (0.36), residues: 508 helix: 3.73 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.85 (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 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4110) covalent geometry : angle 0.38891 ( 5572) hydrogen bonds : bond 0.03976 ( 347) hydrogen bonds : angle 2.81326 ( 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 32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.143 Fit side-chains REVERT: A 80 GLU cc_start: 0.6894 (tt0) cc_final: 0.6580 (mt-10) REVERT: A 198 MET cc_start: 0.6920 (ttp) cc_final: 0.6591 (ttt) REVERT: B 80 GLU cc_start: 0.6887 (tt0) cc_final: 0.6577 (mt-10) REVERT: B 198 MET cc_start: 0.6941 (ttp) cc_final: 0.6612 (ttt) outliers start: 10 outliers final: 6 residues processed: 30 average time/residue: 0.0685 time to fit residues: 2.6757 Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.8980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3896 r_free = 0.3896 target = 0.158950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117534 restraints weight = 4275.591| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.35 r_work: 0.3242 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4110 Z= 0.129 Angle : 0.398 4.878 5572 Z= 0.222 Chirality : 0.034 0.148 638 Planarity : 0.002 0.026 690 Dihedral : 6.714 56.463 592 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.53 % Allowed : 5.05 % 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: 4.98 (0.36), residues: 508 helix: 3.73 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.79 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.009 0.001 TYR A 229 PHE 0.008 0.001 PHE A 232 TRP 0.003 0.001 TRP A 289 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4110) covalent geometry : angle 0.39843 ( 5572) hydrogen bonds : bond 0.04096 ( 347) hydrogen bonds : angle 2.83696 ( 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 : 0.169 Fit side-chains REVERT: A 80 GLU cc_start: 0.6908 (tt0) cc_final: 0.6569 (mt-10) REVERT: A 198 MET cc_start: 0.6922 (ttp) cc_final: 0.6602 (ttt) REVERT: B 80 GLU cc_start: 0.6887 (tt0) cc_final: 0.6554 (mt-10) REVERT: B 198 MET cc_start: 0.6942 (ttp) cc_final: 0.6621 (ttt) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.0779 time to fit residues: 3.0741 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 : 0.096 ------------------------------------------------------------------------------- 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: 0.8980 chunk 8 optimal weight: 0.0060 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.159434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118105 restraints weight = 4231.107| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.34 r_work: 0.3248 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1862 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= 0.123 Angle : 0.391 4.851 5572 Z= 0.219 Chirality : 0.033 0.146 638 Planarity : 0.002 0.025 690 Dihedral : 6.703 56.507 592 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.53 % Allowed : 5.05 % 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: 4.99 (0.36), residues: 508 helix: 3.75 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.74 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 62 TYR 0.008 0.001 TYR B 229 PHE 0.008 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 covalent geometry : bond 0.00281 ( 4110) covalent geometry : angle 0.39130 ( 5572) hydrogen bonds : bond 0.03998 ( 347) hydrogen bonds : angle 2.80363 ( 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 : 0.109 Fit side-chains REVERT: A 80 GLU cc_start: 0.6900 (tt0) cc_final: 0.6557 (mt-10) REVERT: B 80 GLU cc_start: 0.6889 (tt0) cc_final: 0.6550 (mt-10) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.0774 time to fit residues: 3.0445 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 : 0.143 ------------------------------------------------------------------------------- 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: 0.9980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 46 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.159881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118303 restraints weight = 4261.158| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.38 r_work: 0.3256 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1907 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= 0.116 Angle : 0.384 4.859 5572 Z= 0.215 Chirality : 0.033 0.145 638 Planarity : 0.002 0.025 690 Dihedral : 6.674 56.627 592 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 5.04 (0.36), residues: 508 helix: 3.78 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.77 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 62 TYR 0.008 0.001 TYR B 229 PHE 0.007 0.001 PHE A 232 TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4110) covalent geometry : angle 0.38438 ( 5572) hydrogen bonds : bond 0.03927 ( 347) hydrogen bonds : angle 2.78055 ( 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 : 0.145 Fit side-chains REVERT: A 80 GLU cc_start: 0.6898 (tt0) cc_final: 0.6548 (mt-10) REVERT: B 80 GLU cc_start: 0.6890 (tt0) cc_final: 0.6544 (mt-10) outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.0804 time to fit residues: 3.1846 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 : 0.140 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.157705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116432 restraints weight = 4234.100| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.33 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: 0.7541 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4110 Z= 0.147 Angle : 0.418 4.863 5572 Z= 0.232 Chirality : 0.034 0.155 638 Planarity : 0.003 0.025 690 Dihedral : 6.779 57.085 592 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.02 % Allowed : 4.80 % Favored : 93.18 % 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: 3.71 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.70 (0.66), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.009 0.001 TYR A 229 PHE 0.008 0.001 PHE B 232 TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4110) covalent geometry : angle 0.41806 ( 5572) hydrogen bonds : bond 0.04258 ( 347) hydrogen bonds : angle 2.87691 ( 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 : 0.151 Fit side-chains REVERT: A 80 GLU cc_start: 0.6937 (tt0) cc_final: 0.6586 (mt-10) REVERT: B 80 GLU cc_start: 0.6921 (tt0) cc_final: 0.6574 (mt-10) outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.0772 time to fit residues: 3.0379 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 : 0.159 ------------------------------------------------------------------------------- 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: 0.5980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3897 r_free = 0.3897 target = 0.158841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117359 restraints weight = 4224.259| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.35 r_work: 0.3243 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4110 Z= 0.132 Angle : 0.405 4.843 5572 Z= 0.226 Chirality : 0.034 0.148 638 Planarity : 0.002 0.025 690 Dihedral : 6.754 57.102 592 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.02 % Allowed : 4.80 % Favored : 93.18 % 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: 4.98 (0.36), residues: 508 helix: 3.74 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.77 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.008 0.001 TYR A 229 PHE 0.008 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 covalent geometry : bond 0.00307 ( 4110) covalent geometry : angle 0.40464 ( 5572) hydrogen bonds : bond 0.04104 ( 347) hydrogen bonds : angle 2.82588 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 991.39 seconds wall clock time: 17 minutes 41.72 seconds (1061.72 seconds total)