Starting phenix.real_space_refine on Tue Aug 4 13:24:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9k_34570/08_2026/8h9k_34570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9k_34570/08_2026/8h9k_34570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9k_34570/08_2026/8h9k_34570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9k_34570/08_2026/8h9k_34570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9k_34570/08_2026/8h9k_34570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9k_34570/08_2026/8h9k_34570.map" } resolution = 3.51 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= 0.011 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: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 0.74, per 1000 atoms: 0.22 Number of scatterers: 3381 At special positions: 0 Unit cell: (56.21, 102.93, 206.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 634 8.00 N 560 7.00 C 2176 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: 0.31 Conformation dependent library (CDL) restraints added in 142.7 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 1 sheets defined 71.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 120 removed outlier: 3.836A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.884A pdb=" N ARG L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU L 49 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.146A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.706A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 44 removed outlier: 3.800A pdb=" N LEU M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.786A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 235 hydrogen bonds defined for protein. 699 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: 0.44 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1090 1.34 - 1.46: 550 1.46 - 1.57: 1795 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.20e-02 6.94e+03 6.84e+00 bond pdb=" C PHE M 139 " pdb=" N PRO M 140 " ideal model delta sigma weight residual 1.336 1.310 0.026 1.08e-02 8.57e+03 5.77e+00 bond pdb=" N LEU K 16 " pdb=" CA LEU K 16 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.27e-02 6.20e+03 4.84e+00 bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.451 0.055 3.90e-02 6.57e+02 2.02e+00 bond pdb=" CB GLN M 155 " pdb=" CG GLN M 155 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 4044 1.20 - 2.40: 487 2.40 - 3.60: 107 3.60 - 4.80: 27 4.80 - 6.00: 9 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ALA L 85 " pdb=" CA ALA L 85 " pdb=" C ALA L 85 " ideal model delta sigma weight residual 108.45 113.46 -5.01 1.26e+00 6.30e-01 1.58e+01 angle pdb=" C PHE M 127 " pdb=" N ASP M 128 " pdb=" CA ASP M 128 " ideal model delta sigma weight residual 122.38 116.38 6.00 1.81e+00 3.05e-01 1.10e+01 angle pdb=" N SER L 65 " pdb=" CA SER L 65 " pdb=" C SER L 65 " ideal model delta sigma weight residual 113.38 109.56 3.82 1.17e+00 7.31e-01 1.07e+01 angle pdb=" N GLU K 178 " pdb=" CA GLU K 178 " pdb=" C GLU K 178 " ideal model delta sigma weight residual 111.14 107.77 3.37 1.08e+00 8.57e-01 9.76e+00 angle pdb=" N ASP M 11 " pdb=" CA ASP M 11 " pdb=" C ASP M 11 " ideal model delta sigma weight residual 110.48 106.10 4.38 1.48e+00 4.57e-01 8.75e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 1861 16.81 - 33.61: 194 33.61 - 50.42: 41 50.42 - 67.23: 11 67.23 - 84.03: 6 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ARG K 121 " pdb=" C ARG K 121 " pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 318 0.043 - 0.086: 144 0.086 - 0.128: 39 0.128 - 0.171: 4 0.171 - 0.214: 3 Chirality restraints: 508 Sorted by residual: chirality pdb=" CB VAL L 61 " pdb=" CA VAL L 61 " pdb=" CG1 VAL L 61 " pdb=" CG2 VAL L 61 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL K 177 " pdb=" CA VAL K 177 " pdb=" CG1 VAL K 177 " pdb=" CG2 VAL K 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA ASP K 156 " pdb=" N ASP K 156 " pdb=" C ASP K 156 " pdb=" CB ASP K 156 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 82 " -0.009 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE L 82 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE L 82 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE L 82 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE L 82 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 44 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO M 45 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 45 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 45 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 159 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C ILE K 159 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE K 159 " 0.010 2.00e-02 2.50e+03 pdb=" N SER K 160 " 0.009 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 232 2.72 - 3.26: 3567 3.26 - 3.81: 5391 3.81 - 4.35: 6115 4.35 - 4.90: 10122 Nonbonded interactions: 25427 Sorted by model distance: nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.169 3.120 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.217 3.040 nonbonded pdb=" NE2 GLN K 162 " pdb=" O ASN M 59 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG K 121 " pdb=" O ILE M 18 " model vdw 2.282 3.120 nonbonded pdb=" O GLU M 102 " pdb=" OG SER M 105 " model vdw 2.313 3.040 ... (remaining 25422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 9.340 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.600 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 0.055 3456 Z= 0.278 Angle : 0.906 5.996 4674 Z= 0.564 Chirality : 0.051 0.214 508 Planarity : 0.005 0.041 603 Dihedral : 15.467 84.035 1299 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.34 (0.35), residues: 413 helix: -1.04 (0.25), residues: 286 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 40 TYR 0.016 0.002 TYR K 145 PHE 0.030 0.003 PHE L 82 TRP 0.016 0.002 TRP M 53 HIS 0.005 0.001 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.28 ( 3456) covalent geometry : angle 0.90641 / 0.56 ( 4674) hydrogen bonds : bond 0.15448 / 9.24 ( 235) hydrogen bonds : angle 5.69329 / 4.09 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7749 (tttt) REVERT: K 77 PHE cc_start: 0.8620 (t80) cc_final: 0.8264 (t80) REVERT: K 118 VAL cc_start: 0.8101 (p) cc_final: 0.7842 (p) REVERT: K 143 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6898 (mtm-85) REVERT: K 146 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7505 (ttt180) REVERT: K 169 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7861 (tt0) REVERT: L 50 TYR cc_start: 0.3521 (t80) cc_final: 0.3049 (t80) REVERT: M 111 ILE cc_start: 0.8376 (mt) cc_final: 0.8143 (mt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0662 time to fit residues: 9.2714 Evaluate side-chains 78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 88 GLN K 98 GLN K 103 HIS K 115 GLN L 68 GLN M 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.131852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.112790 restraints weight = 8892.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113080 restraints weight = 4188.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114751 restraints weight = 2533.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114638 restraints weight = 1813.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114733 restraints weight = 1561.192| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3456 Z= 0.154 Angle : 0.612 5.048 4674 Z= 0.336 Chirality : 0.043 0.182 508 Planarity : 0.005 0.042 603 Dihedral : 5.297 55.754 452 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.94 % Allowed : 12.96 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.41), residues: 413 helix: 1.27 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -2.13 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 154 TYR 0.016 0.001 TYR K 148 PHE 0.011 0.001 PHE L 93 TRP 0.010 0.001 TRP M 53 HIS 0.004 0.001 HIS K 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 3456) covalent geometry : angle 0.61153 / 0.34 ( 4674) hydrogen bonds : bond 0.05525 / 3.52 ( 235) hydrogen bonds : angle 4.25290 / 3.10 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7558 (tptt) REVERT: K 118 VAL cc_start: 0.8331 (p) cc_final: 0.8057 (p) REVERT: K 143 ARG cc_start: 0.7180 (mtt180) cc_final: 0.6841 (mtm-85) REVERT: K 145 TYR cc_start: 0.7317 (t80) cc_final: 0.7016 (t80) REVERT: K 146 ARG cc_start: 0.7897 (ttm170) cc_final: 0.7424 (ttt180) REVERT: K 163 ASN cc_start: 0.8553 (t0) cc_final: 0.7956 (m-40) REVERT: K 169 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7758 (tt0) REVERT: L 68 GLN cc_start: 0.7649 (tp-100) cc_final: 0.7286 (tp-100) REVERT: M 118 MET cc_start: 0.7820 (tmm) cc_final: 0.7585 (tpp) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.0759 time to fit residues: 8.7208 Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 GLN M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.128976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109269 restraints weight = 8985.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111118 restraints weight = 4447.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111547 restraints weight = 2208.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111655 restraints weight = 2067.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111752 restraints weight = 1634.175| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3456 Z= 0.197 Angle : 0.616 5.480 4674 Z= 0.336 Chirality : 0.044 0.159 508 Planarity : 0.005 0.047 603 Dihedral : 5.317 60.069 452 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.35 % Allowed : 15.21 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.18 (0.41), residues: 413 helix: 1.83 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -1.84 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 154 TYR 0.011 0.001 TYR K 148 PHE 0.010 0.002 PHE K 58 TRP 0.013 0.002 TRP M 53 HIS 0.007 0.002 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 3456) covalent geometry : angle 0.61565 / 0.34 ( 4674) hydrogen bonds : bond 0.05262 / 3.35 ( 235) hydrogen bonds : angle 4.25847 / 3.09 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7646 (tptm) REVERT: K 118 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.7996 (p) REVERT: K 145 TYR cc_start: 0.7480 (t80) cc_final: 0.7135 (t80) REVERT: K 146 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7498 (ttt180) REVERT: K 150 GLU cc_start: 0.8267 (tt0) cc_final: 0.8013 (tt0) REVERT: L 77 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8609 (mttt) REVERT: L 87 MET cc_start: 0.8061 (mpp) cc_final: 0.7755 (mmm) REVERT: M 94 LYS cc_start: 0.8714 (mttm) cc_final: 0.8413 (mttp) REVERT: M 111 ILE cc_start: 0.8549 (mt) cc_final: 0.8344 (mt) REVERT: M 118 MET cc_start: 0.7880 (tmm) cc_final: 0.7575 (tpp) outliers start: 19 outliers final: 14 residues processed: 92 average time/residue: 0.0671 time to fit residues: 7.2687 Evaluate side-chains 84 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.0000 chunk 3 optimal weight: 5.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.130786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109462 restraints weight = 8822.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111454 restraints weight = 4182.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112662 restraints weight = 2450.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113350 restraints weight = 1683.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.113746 restraints weight = 1342.017| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3456 Z= 0.138 Angle : 0.576 5.923 4674 Z= 0.311 Chirality : 0.041 0.179 508 Planarity : 0.004 0.043 603 Dihedral : 5.119 58.282 452 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.51 % Allowed : 17.46 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.84 (0.42), residues: 413 helix: 2.25 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -1.38 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 167 TYR 0.011 0.001 TYR K 148 PHE 0.009 0.001 PHE L 100 TRP 0.008 0.001 TRP M 53 HIS 0.002 0.001 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 3456) covalent geometry : angle 0.57570 / 0.31 ( 4674) hydrogen bonds : bond 0.04916 / 3.15 ( 235) hydrogen bonds : angle 3.99138 / 2.91 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7557 (tptm) REVERT: K 114 GLN cc_start: 0.8111 (mm110) cc_final: 0.7816 (mm-40) REVERT: K 118 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7859 (p) REVERT: K 145 TYR cc_start: 0.7573 (t80) cc_final: 0.7221 (t80) REVERT: K 146 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7532 (ttt180) REVERT: K 150 GLU cc_start: 0.8354 (tt0) cc_final: 0.8067 (tt0) REVERT: L 68 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7661 (tp-100) REVERT: L 77 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8600 (mttt) REVERT: L 87 MET cc_start: 0.7896 (mpp) cc_final: 0.7542 (mmm) REVERT: M 94 LYS cc_start: 0.8721 (mttm) cc_final: 0.8436 (mttp) REVERT: M 111 ILE cc_start: 0.8535 (mt) cc_final: 0.8285 (mt) REVERT: M 118 MET cc_start: 0.7927 (tmm) cc_final: 0.7667 (tpp) outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 0.0507 time to fit residues: 5.7657 Evaluate side-chains 84 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.2201 > 50:) chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 128 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 = 0.4001 r_free = 0.4001 target = 0.129349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.110717 restraints weight = 9023.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.111561 restraints weight = 5483.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.112286 restraints weight = 3989.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.112375 restraints weight = 3095.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112471 restraints weight = 2587.863| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3456 Z= 0.159 Angle : 0.590 5.941 4674 Z= 0.318 Chirality : 0.042 0.160 508 Planarity : 0.005 0.045 603 Dihedral : 5.147 60.321 452 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.07 % Allowed : 16.34 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.99 (0.42), residues: 413 helix: 2.34 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.22 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 167 TYR 0.009 0.001 TYR M 85 PHE 0.009 0.001 PHE L 100 TRP 0.010 0.001 TRP M 53 HIS 0.003 0.001 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 3456) covalent geometry : angle 0.58959 / 0.32 ( 4674) hydrogen bonds : bond 0.04879 / 3.11 ( 235) hydrogen bonds : angle 4.01503 / 2.92 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7582 (tptm) REVERT: K 85 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8107 (tt) REVERT: K 118 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7831 (p) REVERT: K 145 TYR cc_start: 0.7523 (t80) cc_final: 0.7220 (t80) REVERT: K 146 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7492 (ttt180) REVERT: K 150 GLU cc_start: 0.8233 (tt0) cc_final: 0.7973 (tt0) REVERT: L 87 MET cc_start: 0.7954 (mpp) cc_final: 0.7658 (mmm) REVERT: M 19 ILE cc_start: 0.9002 (mm) cc_final: 0.8656 (tp) REVERT: M 94 LYS cc_start: 0.8698 (mttm) cc_final: 0.8421 (mttp) REVERT: M 111 ILE cc_start: 0.8524 (mt) cc_final: 0.8246 (mt) REVERT: M 118 MET cc_start: 0.8032 (tmm) cc_final: 0.7678 (tpp) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.0654 time to fit residues: 6.6062 Evaluate side-chains 84 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.130621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111531 restraints weight = 8969.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113423 restraints weight = 4091.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.114091 restraints weight = 2127.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114286 restraints weight = 1886.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114316 restraints weight = 1464.397| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3456 Z= 0.127 Angle : 0.566 6.429 4674 Z= 0.303 Chirality : 0.041 0.168 508 Planarity : 0.004 0.042 603 Dihedral : 4.944 58.146 452 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.07 % Allowed : 16.34 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.37 (0.42), residues: 413 helix: 2.58 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -0.99 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 167 TYR 0.007 0.001 TYR K 148 PHE 0.010 0.001 PHE L 100 TRP 0.006 0.001 TRP M 33 HIS 0.003 0.001 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 3456) covalent geometry : angle 0.56627 / 0.30 ( 4674) hydrogen bonds : bond 0.04618 / 2.95 ( 235) hydrogen bonds : angle 3.82204 / 2.81 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7821 (mmmt) cc_final: 0.7525 (tptm) REVERT: K 118 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7608 (p) REVERT: K 129 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8773 (ptp-110) REVERT: K 134 MET cc_start: 0.8312 (ttm) cc_final: 0.7929 (ttm) REVERT: K 145 TYR cc_start: 0.7580 (t80) cc_final: 0.7284 (t80) REVERT: K 146 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7552 (ttt180) REVERT: K 150 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7991 (tt0) REVERT: L 49 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6708 (mm-30) REVERT: L 60 PRO cc_start: 0.6757 (Cg_endo) cc_final: 0.6501 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7935 (mm-40) REVERT: L 87 MET cc_start: 0.7810 (mpp) cc_final: 0.7428 (mmm) REVERT: M 19 ILE cc_start: 0.8958 (mm) cc_final: 0.8734 (tp) REVERT: M 94 LYS cc_start: 0.8707 (mttm) cc_final: 0.8441 (mttp) REVERT: M 111 ILE cc_start: 0.8505 (mt) cc_final: 0.8246 (mt) REVERT: M 118 MET cc_start: 0.8041 (tmm) cc_final: 0.7697 (tpp) outliers start: 18 outliers final: 14 residues processed: 90 average time/residue: 0.0845 time to fit residues: 8.9813 Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.130269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109379 restraints weight = 9221.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111417 restraints weight = 4367.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112623 restraints weight = 2539.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113329 restraints weight = 1735.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.113656 restraints weight = 1361.816| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3456 Z= 0.131 Angle : 0.573 6.573 4674 Z= 0.304 Chirality : 0.040 0.179 508 Planarity : 0.004 0.042 603 Dihedral : 4.975 57.736 452 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.35 % Allowed : 17.75 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.42), residues: 413 helix: 2.62 (0.29), residues: 290 sheet: None (None), residues: 0 loop : -0.52 (0.65), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 166 TYR 0.011 0.001 TYR M 85 PHE 0.013 0.001 PHE L 82 TRP 0.006 0.001 TRP M 33 HIS 0.001 0.000 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 3456) covalent geometry : angle 0.57262 / 0.30 ( 4674) hydrogen bonds : bond 0.04514 / 2.89 ( 235) hydrogen bonds : angle 3.78490 / 2.77 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7866 (mmmt) cc_final: 0.7510 (tttm) REVERT: K 118 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7738 (p) REVERT: K 134 MET cc_start: 0.8306 (ttm) cc_final: 0.7895 (ttm) REVERT: K 145 TYR cc_start: 0.7623 (t80) cc_final: 0.7342 (t80) REVERT: K 146 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7549 (ttt180) REVERT: K 150 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7985 (tt0) REVERT: K 167 ARG cc_start: 0.7930 (mmp80) cc_final: 0.7494 (ptt90) REVERT: L 60 PRO cc_start: 0.6778 (Cg_endo) cc_final: 0.6522 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7778 (mm-40) REVERT: L 72 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8094 (mm-30) REVERT: L 87 MET cc_start: 0.7771 (mpp) cc_final: 0.7427 (mmm) REVERT: M 94 LYS cc_start: 0.8686 (mttm) cc_final: 0.8425 (mttp) REVERT: M 111 ILE cc_start: 0.8478 (mt) cc_final: 0.8208 (mt) REVERT: M 118 MET cc_start: 0.8055 (tmm) cc_final: 0.7700 (tpp) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 0.0598 time to fit residues: 6.1466 Evaluate side-chains 81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 162 GLN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 0.0040 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.129991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.112114 restraints weight = 9102.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112634 restraints weight = 5703.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113716 restraints weight = 4173.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113751 restraints weight = 3097.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114027 restraints weight = 2625.830| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3456 Z= 0.140 Angle : 0.620 8.443 4674 Z= 0.327 Chirality : 0.041 0.186 508 Planarity : 0.005 0.042 603 Dihedral : 4.998 57.338 452 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.79 % Allowed : 18.87 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.67 (0.43), residues: 413 helix: 2.70 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -0.55 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 143 TYR 0.012 0.001 TYR M 85 PHE 0.040 0.002 PHE L 82 TRP 0.006 0.001 TRP M 33 HIS 0.002 0.001 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 3456) covalent geometry : angle 0.61959 / 0.33 ( 4674) hydrogen bonds : bond 0.04571 / 2.90 ( 235) hydrogen bonds : angle 3.83440 / 2.79 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7503 (tttm) REVERT: K 134 MET cc_start: 0.8200 (ttm) cc_final: 0.7886 (ttm) REVERT: K 145 TYR cc_start: 0.7549 (t80) cc_final: 0.7315 (t80) REVERT: K 146 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7536 (ttt180) REVERT: K 150 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7948 (tt0) REVERT: K 167 ARG cc_start: 0.7869 (mmp80) cc_final: 0.7606 (ptt90) REVERT: L 60 PRO cc_start: 0.6668 (Cg_endo) cc_final: 0.6404 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7765 (mm-40) REVERT: L 87 MET cc_start: 0.7789 (mpp) cc_final: 0.7445 (mmm) REVERT: M 94 LYS cc_start: 0.8689 (mttm) cc_final: 0.8431 (mttp) REVERT: M 111 ILE cc_start: 0.8467 (mt) cc_final: 0.8199 (mt) REVERT: M 118 MET cc_start: 0.8078 (tmm) cc_final: 0.7736 (tpp) outliers start: 17 outliers final: 16 residues processed: 83 average time/residue: 0.0902 time to fit residues: 8.8219 Evaluate side-chains 85 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 162 GLN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108199 restraints weight = 9148.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110140 restraints weight = 4440.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111345 restraints weight = 2618.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111948 restraints weight = 1793.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.112407 restraints weight = 1436.589| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 3456 Z= 0.172 Angle : 0.648 8.553 4674 Z= 0.342 Chirality : 0.043 0.187 508 Planarity : 0.005 0.042 603 Dihedral : 5.125 60.634 452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.35 % Allowed : 18.31 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.52 (0.42), residues: 413 helix: 2.57 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.55 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 143 TYR 0.011 0.001 TYR M 85 PHE 0.043 0.002 PHE L 82 TRP 0.005 0.001 TRP M 33 HIS 0.003 0.001 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 3456) covalent geometry : angle 0.64775 / 0.34 ( 4674) hydrogen bonds : bond 0.04714 / 2.99 ( 235) hydrogen bonds : angle 3.96851 / 2.88 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7557 (tttm) REVERT: K 85 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8082 (tt) REVERT: K 134 MET cc_start: 0.8345 (ttm) cc_final: 0.7913 (ttm) REVERT: K 145 TYR cc_start: 0.7655 (t80) cc_final: 0.7400 (t80) REVERT: K 146 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7616 (ttt180) REVERT: L 60 PRO cc_start: 0.6655 (Cg_endo) cc_final: 0.6385 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7935 (mm-40) REVERT: L 87 MET cc_start: 0.7736 (mpp) cc_final: 0.7365 (mmm) REVERT: M 94 LYS cc_start: 0.8710 (mttm) cc_final: 0.8448 (mttp) REVERT: M 111 ILE cc_start: 0.8484 (mt) cc_final: 0.8205 (mt) REVERT: M 118 MET cc_start: 0.8069 (tmm) cc_final: 0.7713 (tpp) outliers start: 19 outliers final: 15 residues processed: 88 average time/residue: 0.0636 time to fit residues: 6.6271 Evaluate side-chains 85 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 162 GLN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.131541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111355 restraints weight = 9099.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.113369 restraints weight = 4298.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.114565 restraints weight = 2474.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115226 restraints weight = 1684.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115627 restraints weight = 1332.899| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 3456 Z= 0.142 Angle : 0.642 8.784 4674 Z= 0.342 Chirality : 0.042 0.196 508 Planarity : 0.004 0.041 603 Dihedral : 4.870 56.506 452 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.94 % Allowed : 19.72 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.67 (0.42), residues: 413 helix: 2.66 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -0.44 (0.62), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 143 TYR 0.014 0.001 TYR M 85 PHE 0.022 0.001 PHE L 82 TRP 0.007 0.001 TRP M 12 HIS 0.004 0.001 HIS K 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 3456) covalent geometry : angle 0.64179 / 0.34 ( 4674) hydrogen bonds : bond 0.04546 / 2.88 ( 235) hydrogen bonds : angle 3.77414 / 2.77 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7518 (tptm) REVERT: K 145 TYR cc_start: 0.7642 (t80) cc_final: 0.7397 (t80) REVERT: K 146 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7625 (ttt180) REVERT: K 167 ARG cc_start: 0.7959 (mmp80) cc_final: 0.7541 (ptt90) REVERT: L 60 PRO cc_start: 0.6707 (Cg_endo) cc_final: 0.6462 (Cg_exo) REVERT: M 111 ILE cc_start: 0.8417 (mt) cc_final: 0.8145 (mt) REVERT: M 118 MET cc_start: 0.8072 (tmm) cc_final: 0.7736 (tpp) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.0934 time to fit residues: 9.3935 Evaluate side-chains 79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.130710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112090 restraints weight = 9095.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.113541 restraints weight = 4486.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114374 restraints weight = 2469.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114552 restraints weight = 2115.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114634 restraints weight = 1703.464| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 3456 Z= 0.142 Angle : 0.674 10.020 4674 Z= 0.349 Chirality : 0.042 0.206 508 Planarity : 0.005 0.045 603 Dihedral : 4.817 54.498 452 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.38 % Allowed : 20.00 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.87 (0.42), residues: 413 helix: 2.92 (0.29), residues: 277 sheet: None (None), residues: 0 loop : -0.33 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 141 TYR 0.012 0.001 TYR L 50 PHE 0.064 0.002 PHE L 82 TRP 0.007 0.001 TRP M 33 HIS 0.002 0.001 HIS K 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3456) covalent geometry : angle 0.67395 / 0.35 ( 4674) hydrogen bonds : bond 0.04544 / 2.87 ( 235) hydrogen bonds : angle 3.73655 / 2.74 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1107.85 seconds wall clock time: 19 minutes 57.76 seconds (1197.76 seconds total)