Starting phenix.real_space_refine on Tue Feb 3 15:02:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muh_48632/02_2026/9muh_48632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muh_48632/02_2026/9muh_48632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9muh_48632/02_2026/9muh_48632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muh_48632/02_2026/9muh_48632.map" model { file = "/net/cci-nas-00/data/ceres_data/9muh_48632/02_2026/9muh_48632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muh_48632/02_2026/9muh_48632.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 28 5.16 5 C 2676 2.51 5 N 664 2.21 5 O 692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 4062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1995 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1995 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' K': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.15, per 1000 atoms: 0.28 Number of scatterers: 4062 At special positions: 0 Unit cell: (91.176, 71.264, 82.792, 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 28 16.00 O 692 8.00 N 664 7.00 C 2676 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: 0.22 Conformation dependent library (CDL) restraints added in 90.8 milliseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 85.5% 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 2 through 52 removed outlier: 5.545A pdb=" N GLU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 148 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 242 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'B' and resid 2 through 52 removed outlier: 5.546A pdb=" N GLU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Proline residue: B 33 - end of helix Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 148 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 242 Processing helix chain 'B' and resid 242 through 249 334 hydrogen bonds defined for protein. 1002 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: 0.62 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 606 1.32 - 1.44: 1206 1.44 - 1.56: 2300 1.56 - 1.68: 0 1.68 - 1.81: 46 Bond restraints: 4158 Sorted by residual: bond pdb=" N HIS A 98 " pdb=" CA HIS A 98 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.23e-02 6.61e+03 7.92e+00 bond pdb=" N HIS B 98 " pdb=" CA HIS B 98 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" N GLN A 77 " pdb=" CA GLN A 77 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.31e-02 5.83e+03 7.13e+00 bond pdb=" N GLN B 77 " pdb=" CA GLN B 77 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.79e+00 bond pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.31e-02 5.83e+03 4.61e+00 ... (remaining 4153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 5375 1.05 - 2.10: 209 2.10 - 3.15: 39 3.15 - 4.20: 8 4.20 - 5.26: 7 Bond angle restraints: 5638 Sorted by residual: angle pdb=" N GLY B 97 " pdb=" CA GLY B 97 " pdb=" C GLY B 97 " ideal model delta sigma weight residual 114.69 110.82 3.87 1.19e+00 7.06e-01 1.06e+01 angle pdb=" CA HIS A 98 " pdb=" CB HIS A 98 " pdb=" CG HIS A 98 " ideal model delta sigma weight residual 113.80 110.68 3.12 1.00e+00 1.00e+00 9.73e+00 angle pdb=" CA ALA A 99 " pdb=" C ALA A 99 " pdb=" O ALA A 99 " ideal model delta sigma weight residual 121.81 118.18 3.63 1.18e+00 7.18e-01 9.46e+00 angle pdb=" CA ALA B 99 " pdb=" C ALA B 99 " pdb=" O ALA B 99 " ideal model delta sigma weight residual 121.81 118.20 3.61 1.18e+00 7.18e-01 9.37e+00 angle pdb=" N GLY A 97 " pdb=" CA GLY A 97 " pdb=" C GLY A 97 " ideal model delta sigma weight residual 114.69 111.07 3.62 1.19e+00 7.06e-01 9.27e+00 ... (remaining 5633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 2307 13.84 - 27.68: 175 27.68 - 41.52: 24 41.52 - 55.36: 6 55.36 - 69.20: 4 Dihedral angle restraints: 2516 sinusoidal: 1070 harmonic: 1446 Sorted by residual: dihedral pdb=" CA TRP B 78 " pdb=" C TRP B 78 " pdb=" N ARG B 79 " pdb=" CA ARG B 79 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TRP A 78 " pdb=" C TRP A 78 " pdb=" N ARG A 79 " pdb=" CA ARG A 79 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" N ARG A 142 " pdb=" CA ARG A 142 " pdb=" CB ARG A 142 " pdb=" CG ARG A 142 " ideal model delta sinusoidal sigma weight residual -60.00 -115.61 55.61 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 2513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 358 0.024 - 0.047: 148 0.047 - 0.070: 98 0.070 - 0.094: 19 0.094 - 0.117: 19 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA THR B 93 " pdb=" N THR B 93 " pdb=" C THR B 93 " pdb=" CB THR B 93 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA VAL B 154 " pdb=" N VAL B 154 " pdb=" C VAL B 154 " pdb=" CB VAL B 154 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 639 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 32 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO B 33 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 33 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 33 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 32 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 33 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 33 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 33 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 27 " -0.005 2.00e-02 2.50e+03 9.91e-03 9.82e-01 pdb=" C ASP A 27 " 0.017 2.00e-02 2.50e+03 pdb=" O ASP A 27 " -0.006 2.00e-02 2.50e+03 pdb=" N ALA A 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1431 2.85 - 3.43: 4753 3.43 - 4.00: 7894 4.00 - 4.57: 11352 4.57 - 5.14: 15899 Nonbonded interactions: 41329 Sorted by model distance: nonbonded pdb=" O ILE A 88 " pdb=" OG1 THR A 92 " model vdw 2.283 3.040 nonbonded pdb=" O ILE B 88 " pdb=" OG1 THR B 92 " model vdw 2.283 3.040 nonbonded pdb=" O ASP A 211 " pdb=" OG1 THR A 216 " model vdw 2.332 3.040 nonbonded pdb=" O ASP B 211 " pdb=" OG1 THR B 216 " model vdw 2.332 3.040 nonbonded pdb=" O VAL B 76 " pdb=" NE2 GLN B 215 " model vdw 2.373 3.120 ... (remaining 41324 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 1 through 249) selection = (chain 'B' and resid 1 through 249) } 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: 1.630 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.210 Find NCS groups from input model: 0.060 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4158 Z= 0.180 Angle : 0.511 5.255 5638 Z= 0.299 Chirality : 0.037 0.117 642 Planarity : 0.003 0.026 690 Dihedral : 10.074 69.204 1596 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.48 % Allowed : 1.20 % Favored : 98.32 % 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: 2.61 (0.35), residues: 494 helix: 2.37 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.58 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 40 TYR 0.010 0.001 TYR A 227 PHE 0.014 0.001 PHE B 223 TRP 0.007 0.001 TRP B 78 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4158) covalent geometry : angle 0.51130 ( 5638) hydrogen bonds : bond 0.05282 ( 334) hydrogen bonds : angle 4.07057 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASN cc_start: 0.7307 (t0) cc_final: 0.6951 (t0) outliers start: 2 outliers final: 1 residues processed: 148 average time/residue: 0.0650 time to fit residues: 11.4294 Evaluate side-chains 90 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 133 ASN B 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.222475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.194356 restraints weight = 4442.999| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.58 r_work: 0.4244 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4158 Z= 0.178 Angle : 0.584 5.051 5638 Z= 0.311 Chirality : 0.040 0.140 642 Planarity : 0.004 0.023 690 Dihedral : 6.242 58.957 703 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.40 % Allowed : 6.49 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.09 (0.36), residues: 494 helix: 2.72 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.56 (0.58), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 49 TYR 0.026 0.002 TYR B 18 PHE 0.018 0.002 PHE A 109 TRP 0.005 0.001 TRP B 78 HIS 0.013 0.002 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 4158) covalent geometry : angle 0.58402 ( 5638) hydrogen bonds : bond 0.04333 ( 334) hydrogen bonds : angle 4.03770 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7360 (ttm170) REVERT: A 249 MET cc_start: 0.3751 (mmt) cc_final: 0.2751 (ptt) REVERT: B 4 GLN cc_start: 0.5069 (mp10) cc_final: 0.4464 (mm-40) REVERT: B 195 ILE cc_start: 0.7940 (mm) cc_final: 0.7723 (pt) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.0496 time to fit residues: 6.4826 Evaluate side-chains 91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN B 133 ASN B 209 GLN B 217 GLN B 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.218763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.190245 restraints weight = 4373.619| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.58 r_work: 0.4206 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4158 Z= 0.183 Angle : 0.574 6.020 5638 Z= 0.309 Chirality : 0.040 0.137 642 Planarity : 0.003 0.024 690 Dihedral : 5.913 59.903 702 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.16 % Allowed : 9.86 % Favored : 87.98 % 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: 3.04 (0.36), residues: 494 helix: 2.68 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -1.46 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 7 TYR 0.021 0.002 TYR B 227 PHE 0.013 0.002 PHE A 202 TRP 0.005 0.001 TRP B 78 HIS 0.011 0.002 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4158) covalent geometry : angle 0.57412 ( 5638) hydrogen bonds : bond 0.04389 ( 334) hydrogen bonds : angle 4.12398 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7729 (mm) cc_final: 0.7470 (mp) REVERT: A 159 MET cc_start: 0.7367 (tpt) cc_final: 0.7106 (tpt) REVERT: A 249 MET cc_start: 0.4039 (mmt) cc_final: 0.3008 (ptt) REVERT: B 186 PHE cc_start: 0.8356 (t80) cc_final: 0.8110 (t80) REVERT: B 195 ILE cc_start: 0.7962 (mm) cc_final: 0.7712 (pt) REVERT: B 217 GLN cc_start: 0.7844 (mt0) cc_final: 0.7578 (mt0) outliers start: 9 outliers final: 5 residues processed: 103 average time/residue: 0.0742 time to fit residues: 9.4366 Evaluate side-chains 89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN A 240 ASN B 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.221490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.193429 restraints weight = 4380.756| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 1.61 r_work: 0.4237 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4158 Z= 0.132 Angle : 0.521 5.498 5638 Z= 0.282 Chirality : 0.038 0.128 642 Planarity : 0.003 0.022 690 Dihedral : 5.551 59.769 702 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.64 % Allowed : 12.26 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.36), residues: 494 helix: 2.81 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.46 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.020 0.002 TYR B 192 PHE 0.015 0.001 PHE A 223 TRP 0.006 0.001 TRP B 78 HIS 0.009 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4158) covalent geometry : angle 0.52145 ( 5638) hydrogen bonds : bond 0.04060 ( 334) hydrogen bonds : angle 3.98462 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.093 Fit side-chains REVERT: A 46 LEU cc_start: 0.7846 (mm) cc_final: 0.7426 (mp) REVERT: A 79 ARG cc_start: 0.7405 (ttt-90) cc_final: 0.7060 (ttp80) REVERT: A 159 MET cc_start: 0.6995 (tpt) cc_final: 0.6425 (tpt) REVERT: B 4 GLN cc_start: 0.4899 (mp10) cc_final: 0.4475 (mm-40) REVERT: B 18 TYR cc_start: 0.6776 (t80) cc_final: 0.6544 (t80) outliers start: 11 outliers final: 2 residues processed: 100 average time/residue: 0.0579 time to fit residues: 7.2151 Evaluate side-chains 87 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.0370 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.219561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.191112 restraints weight = 4408.913| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 1.62 r_work: 0.4216 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4074 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4158 Z= 0.155 Angle : 0.554 7.096 5638 Z= 0.296 Chirality : 0.039 0.130 642 Planarity : 0.003 0.024 690 Dihedral : 5.473 56.532 702 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.16 % Allowed : 14.90 % Favored : 82.93 % 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: 3.05 (0.36), residues: 494 helix: 2.72 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.68 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 145 TYR 0.023 0.002 TYR B 192 PHE 0.014 0.002 PHE A 223 TRP 0.005 0.001 TRP B 78 HIS 0.009 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4158) covalent geometry : angle 0.55398 ( 5638) hydrogen bonds : bond 0.04200 ( 334) hydrogen bonds : angle 4.00790 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.147 Fit side-chains REVERT: A 46 LEU cc_start: 0.7900 (mm) cc_final: 0.7497 (mp) REVERT: A 249 MET cc_start: 0.3646 (mmt) cc_final: 0.2775 (ptt) REVERT: B 4 GLN cc_start: 0.4914 (mp10) cc_final: 0.4509 (mm-40) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.0672 time to fit residues: 7.8723 Evaluate side-chains 86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.219936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.192917 restraints weight = 4375.949| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.52 r_work: 0.4232 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4158 Z= 0.144 Angle : 0.546 6.165 5638 Z= 0.291 Chirality : 0.039 0.155 642 Planarity : 0.004 0.051 690 Dihedral : 5.361 54.032 702 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 16.59 % Favored : 81.97 % 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: 3.00 (0.36), residues: 494 helix: 2.67 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.64 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 145 TYR 0.025 0.002 TYR A 192 PHE 0.014 0.002 PHE A 223 TRP 0.007 0.001 TRP A 78 HIS 0.011 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4158) covalent geometry : angle 0.54602 ( 5638) hydrogen bonds : bond 0.04144 ( 334) hydrogen bonds : angle 4.01566 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.152 Fit side-chains REVERT: A 46 LEU cc_start: 0.7888 (mm) cc_final: 0.7442 (mp) REVERT: A 192 TYR cc_start: 0.8594 (t80) cc_final: 0.8371 (t80) REVERT: A 249 MET cc_start: 0.3705 (mmt) cc_final: 0.3031 (ptt) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.0608 time to fit residues: 6.9714 Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.218588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.190439 restraints weight = 4460.434| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 1.61 r_work: 0.4194 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4158 Z= 0.163 Angle : 0.572 6.567 5638 Z= 0.306 Chirality : 0.039 0.135 642 Planarity : 0.003 0.030 690 Dihedral : 5.389 47.077 702 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.92 % Allowed : 15.87 % Favored : 82.21 % 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: 2.91 (0.36), residues: 494 helix: 2.59 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.57 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.020 0.002 TYR A 18 PHE 0.016 0.002 PHE A 135 TRP 0.005 0.001 TRP B 78 HIS 0.013 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4158) covalent geometry : angle 0.57231 ( 5638) hydrogen bonds : bond 0.04278 ( 334) hydrogen bonds : angle 4.05488 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7845 (mm) cc_final: 0.7374 (mp) REVERT: A 192 TYR cc_start: 0.8700 (t80) cc_final: 0.8366 (t80) REVERT: B 18 TYR cc_start: 0.7042 (t80) cc_final: 0.6813 (t80) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 0.0487 time to fit residues: 5.6749 Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.218961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.190623 restraints weight = 4408.211| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 1.60 r_work: 0.4209 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4158 Z= 0.156 Angle : 0.593 13.077 5638 Z= 0.307 Chirality : 0.039 0.133 642 Planarity : 0.003 0.022 690 Dihedral : 5.374 43.594 702 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.20 % Allowed : 16.11 % Favored : 82.69 % 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: 2.84 (0.36), residues: 494 helix: 2.54 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.58 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.019 0.002 TYR B 192 PHE 0.014 0.002 PHE A 223 TRP 0.007 0.001 TRP B 78 HIS 0.013 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4158) covalent geometry : angle 0.59327 ( 5638) hydrogen bonds : bond 0.04258 ( 334) hydrogen bonds : angle 4.07257 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7824 (mm) cc_final: 0.7377 (mp) REVERT: A 98 HIS cc_start: 0.6194 (t70) cc_final: 0.5853 (t70) REVERT: B 249 MET cc_start: 0.2652 (tpp) cc_final: 0.2361 (tpt) outliers start: 5 outliers final: 5 residues processed: 85 average time/residue: 0.0619 time to fit residues: 6.6681 Evaluate side-chains 83 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.218666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.190276 restraints weight = 4472.533| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.67 r_work: 0.4206 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4069 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4158 Z= 0.161 Angle : 0.595 12.313 5638 Z= 0.310 Chirality : 0.039 0.136 642 Planarity : 0.003 0.022 690 Dihedral : 5.423 43.973 702 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.44 % Allowed : 16.35 % Favored : 82.21 % 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: 2.89 (0.36), residues: 494 helix: 2.56 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.40 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.022 0.002 TYR A 18 PHE 0.014 0.002 PHE A 223 TRP 0.006 0.001 TRP B 78 HIS 0.012 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4158) covalent geometry : angle 0.59493 ( 5638) hydrogen bonds : bond 0.04281 ( 334) hydrogen bonds : angle 4.06780 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.095 Fit side-chains REVERT: A 46 LEU cc_start: 0.7818 (mm) cc_final: 0.7356 (mp) REVERT: A 79 ARG cc_start: 0.7363 (ttt-90) cc_final: 0.6967 (ttp80) REVERT: A 249 MET cc_start: 0.3775 (mmt) cc_final: 0.3314 (ptt) REVERT: B 249 MET cc_start: 0.2584 (tpp) cc_final: 0.2334 (tpt) outliers start: 6 outliers final: 5 residues processed: 83 average time/residue: 0.0536 time to fit residues: 5.6218 Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.218081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.190359 restraints weight = 4360.270| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 1.59 r_work: 0.4199 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4158 Z= 0.166 Angle : 0.616 12.223 5638 Z= 0.323 Chirality : 0.040 0.135 642 Planarity : 0.003 0.022 690 Dihedral : 5.494 44.438 702 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.20 % Allowed : 17.31 % Favored : 81.49 % 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: 2.74 (0.36), residues: 494 helix: 2.47 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.59 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.020 0.002 TYR B 192 PHE 0.014 0.002 PHE A 223 TRP 0.006 0.001 TRP B 78 HIS 0.011 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4158) covalent geometry : angle 0.61632 ( 5638) hydrogen bonds : bond 0.04350 ( 334) hydrogen bonds : angle 4.10020 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.151 Fit side-chains REVERT: A 46 LEU cc_start: 0.7791 (mm) cc_final: 0.7348 (mp) REVERT: A 249 MET cc_start: 0.3733 (mmt) cc_final: 0.3197 (ptt) REVERT: B 192 TYR cc_start: 0.8111 (t80) cc_final: 0.7859 (t80) REVERT: B 249 MET cc_start: 0.2163 (tpp) cc_final: 0.1882 (tpt) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.0506 time to fit residues: 5.0743 Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.218551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.191026 restraints weight = 4345.958| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 1.47 r_work: 0.4208 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4158 Z= 0.152 Angle : 0.591 11.247 5638 Z= 0.311 Chirality : 0.039 0.132 642 Planarity : 0.003 0.022 690 Dihedral : 5.503 44.436 702 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.20 % Allowed : 17.31 % Favored : 81.49 % 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: 2.80 (0.36), residues: 494 helix: 2.51 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.58 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.021 0.002 TYR A 18 PHE 0.014 0.002 PHE A 223 TRP 0.007 0.001 TRP B 78 HIS 0.009 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4158) covalent geometry : angle 0.59101 ( 5638) hydrogen bonds : bond 0.04254 ( 334) hydrogen bonds : angle 4.05154 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1152.48 seconds wall clock time: 20 minutes 18.43 seconds (1218.43 seconds total)