Starting phenix.real_space_refine on Thu Mar 6 05:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bgu_16036/03_2025/8bgu_16036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgu_16036/03_2025/8bgu_16036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bgu_16036/03_2025/8bgu_16036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgu_16036/03_2025/8bgu_16036.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgu_16036/03_2025/8bgu_16036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgu_16036/03_2025/8bgu_16036.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 P 121 5.49 5 C 2457 2.51 5 N 908 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4779 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 36} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 51} Link IDs: {'rna2p': 13, 'rna3p': 107} Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1128 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 637 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 17, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 420 Chain: "B" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 861 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 169} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 14, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 325 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.87, per 1000 atoms: 0.81 Number of scatterers: 4779 At special positions: 0 Unit cell: (78.366, 102.723, 130.257, 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) Zn 1 29.99 P 121 15.00 O 1292 8.00 N 908 7.00 C 2457 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: 1.25 Conformation dependent library (CDL) restraints added in 412.8 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 35.1% alpha, 10.7% beta 40 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'F' and resid 298 through 302 Processing helix chain 'A' and resid 81 through 86 Proline residue: A 84 - end of helix No H-bonds generated for 'chain 'A' and resid 81 through 86' Processing helix chain 'A' and resid 94 through 114 Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 235 through 250 Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.593A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 138 through 144 removed outlier: 3.525A pdb=" N ILE B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA B 142 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 144 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 Processing sheet with id=AA1, first strand: chain 'F' and resid 303 through 304 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 79 removed outlier: 4.751A pdb=" N ASP A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG A 68 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 74 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR A 66 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 184 removed outlier: 3.559A pdb=" N GLU A 189 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 25 128 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 567 1.30 - 1.38: 1132 1.38 - 1.46: 1169 1.46 - 1.54: 1922 1.54 - 1.62: 289 Bond restraints: 5079 Sorted by residual: bond pdb=" C3' G 3 52 " pdb=" O3' G 3 52 " ideal model delta sigma weight residual 1.417 1.442 -0.025 1.50e-02 4.44e+03 2.76e+00 bond pdb=" CA GLY A 87 " pdb=" C GLY A 87 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.35e+00 bond pdb=" C3' C 3 98 " pdb=" O3' C 3 98 " ideal model delta sigma weight residual 1.417 1.439 -0.022 1.50e-02 4.44e+03 2.21e+00 bond pdb=" N GLY A 87 " pdb=" CA GLY A 87 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.77e+00 bond pdb=" N1 C 3 18 " pdb=" C2 C 3 18 " ideal model delta sigma weight residual 1.397 1.420 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 5074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 7188 1.65 - 3.31: 272 3.31 - 4.96: 54 4.96 - 6.62: 18 6.62 - 8.27: 7 Bond angle restraints: 7539 Sorted by residual: angle pdb=" C GLU B 9 " pdb=" N ASN B 10 " pdb=" CA ASN B 10 " ideal model delta sigma weight residual 120.06 127.14 -7.08 1.19e+00 7.06e-01 3.54e+01 angle pdb=" O3' C 3 98 " pdb=" C3' C 3 98 " pdb=" C2' C 3 98 " ideal model delta sigma weight residual 113.70 121.40 -7.70 1.50e+00 4.44e-01 2.63e+01 angle pdb=" O3' G 3 52 " pdb=" C3' G 3 52 " pdb=" C2' G 3 52 " ideal model delta sigma weight residual 113.70 120.98 -7.28 1.50e+00 4.44e-01 2.36e+01 angle pdb=" C3' G 3 52 " pdb=" O3' G 3 52 " pdb=" P U 3 53 " ideal model delta sigma weight residual 120.20 126.68 -6.48 1.50e+00 4.44e-01 1.87e+01 angle pdb=" N GLY A 87 " pdb=" CA GLY A 87 " pdb=" C GLY A 87 " ideal model delta sigma weight residual 111.67 115.60 -3.93 9.20e-01 1.18e+00 1.83e+01 ... (remaining 7534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 2797 32.82 - 65.64: 300 65.64 - 98.46: 45 98.46 - 131.28: 2 131.28 - 164.10: 1 Dihedral angle restraints: 3145 sinusoidal: 1879 harmonic: 1266 Sorted by residual: dihedral pdb=" O4' U 3 121 " pdb=" C1' U 3 121 " pdb=" N1 U 3 121 " pdb=" C2 U 3 121 " ideal model delta sinusoidal sigma weight residual -128.00 36.10 -164.10 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" CA LEU B 94 " pdb=" C LEU B 94 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" C4' C 3 98 " pdb=" C3' C 3 98 " pdb=" O3' C 3 98 " pdb=" P G 3 99 " ideal model delta sinusoidal sigma weight residual 220.00 98.39 121.61 1 3.50e+01 8.16e-04 1.19e+01 ... (remaining 3142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 926 0.069 - 0.138: 87 0.138 - 0.207: 1 0.207 - 0.276: 0 0.276 - 0.345: 2 Chirality restraints: 1016 Sorted by residual: chirality pdb=" C3' C 3 98 " pdb=" C4' C 3 98 " pdb=" O3' C 3 98 " pdb=" C2' C 3 98 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C3' G 3 52 " pdb=" C4' G 3 52 " pdb=" O3' G 3 52 " pdb=" C2' G 3 52 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1' G 3 5 " pdb=" O4' G 3 5 " pdb=" C2' G 3 5 " pdb=" N9 G 3 5 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1013 not shown) Planarity restraints: 565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 3 92 " -0.024 2.00e-02 2.50e+03 1.11e-02 3.40e+00 pdb=" N9 A 3 92 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A 3 92 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 3 92 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A 3 92 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 3 92 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 3 92 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A 3 92 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 3 67 " 0.024 2.00e-02 2.50e+03 1.01e-02 3.05e+00 pdb=" N9 G 3 67 " -0.018 2.00e-02 2.50e+03 pdb=" C8 G 3 67 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G 3 67 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 3 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G 3 67 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G 3 67 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G 3 67 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 3 67 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G 3 67 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G 3 67 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G 3 67 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 191 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ASN A 191 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN A 191 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 192 " 0.010 2.00e-02 2.50e+03 ... (remaining 562 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 909 2.77 - 3.30: 3973 3.30 - 3.83: 9635 3.83 - 4.37: 9745 4.37 - 4.90: 13364 Nonbonded interactions: 37626 Sorted by model distance: nonbonded pdb=" O6 G 3 1 " pdb=" O4 U 3 121 " model vdw 2.235 3.040 nonbonded pdb=" O2' G 3 77 " pdb=" O6 G 3 101 " model vdw 2.323 3.040 nonbonded pdb=" O6 G 3 67 " pdb=" O4 U 3 111 " model vdw 2.329 2.432 nonbonded pdb=" O2 U 3 81 " pdb=" N2 G 3 99 " model vdw 2.333 2.496 nonbonded pdb=" O4 U 3 81 " pdb=" O6 G 3 99 " model vdw 2.379 2.432 ... (remaining 37621 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: 0.010 Normalize map: mean=0, sd=1: 0.600 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.830 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.025 5079 Z= 0.190 Angle : 0.839 8.272 7539 Z= 0.452 Chirality : 0.041 0.345 1016 Planarity : 0.003 0.017 565 Dihedral : 23.471 164.097 2323 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.34), residues: 441 helix: -1.54 (0.31), residues: 142 sheet: -0.77 (0.74), residues: 55 loop : -2.07 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.308 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0505 time to fit residues: 1.5801 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.031009 restraints weight = 56277.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031810 restraints weight = 33106.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.032319 restraints weight = 23479.305| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 5079 Z= 0.424 Angle : 0.798 6.017 7539 Z= 0.423 Chirality : 0.044 0.248 1016 Planarity : 0.004 0.015 565 Dihedral : 24.363 162.575 2323 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 29.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.39), residues: 441 helix: 0.33 (0.42), residues: 143 sheet: -1.23 (0.68), residues: 54 loop : -1.83 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0557 time to fit residues: 1.8593 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.042821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.030394 restraints weight = 58220.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.031154 restraints weight = 33476.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031691 restraints weight = 23672.799| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 5079 Z= 0.390 Angle : 0.740 6.344 7539 Z= 0.396 Chirality : 0.043 0.235 1016 Planarity : 0.003 0.011 565 Dihedral : 24.568 161.686 2323 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.38), residues: 441 helix: 0.00 (0.42), residues: 149 sheet: -1.31 (0.82), residues: 42 loop : -2.23 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.311 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0469 time to fit residues: 1.5533 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.042927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030502 restraints weight = 57373.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.031260 restraints weight = 33124.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.031830 restraints weight = 23434.124| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 5079 Z= 0.330 Angle : 0.669 5.446 7539 Z= 0.355 Chirality : 0.040 0.232 1016 Planarity : 0.003 0.009 565 Dihedral : 24.276 159.208 2323 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.39), residues: 441 helix: 0.57 (0.44), residues: 143 sheet: -1.33 (0.82), residues: 40 loop : -2.06 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.304 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0472 time to fit residues: 1.5801 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 50.0000 chunk 44 optimal weight: 30.0000 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 7.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.041849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.029697 restraints weight = 59291.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.030439 restraints weight = 34055.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030970 restraints weight = 23946.780| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 5079 Z= 0.402 Angle : 0.754 6.586 7539 Z= 0.401 Chirality : 0.043 0.240 1016 Planarity : 0.003 0.011 565 Dihedral : 24.548 159.709 2323 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 31.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.39), residues: 441 helix: 0.12 (0.43), residues: 142 sheet: -1.49 (0.82), residues: 40 loop : -2.16 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0481 time to fit residues: 1.6242 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 overall best weight: 4.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.043190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.030533 restraints weight = 56460.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.031433 restraints weight = 30746.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.032014 restraints weight = 20829.025| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 5079 Z= 0.223 Angle : 0.570 5.181 7539 Z= 0.303 Chirality : 0.036 0.225 1016 Planarity : 0.002 0.008 565 Dihedral : 23.883 161.187 2323 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.40), residues: 441 helix: 1.03 (0.45), residues: 143 sheet: -1.45 (1.04), residues: 28 loop : -1.80 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0519 time to fit residues: 1.6962 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.0030 chunk 42 optimal weight: 6.9990 overall best weight: 5.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.030329 restraints weight = 57496.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.031125 restraints weight = 32720.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.031648 restraints weight = 22905.241| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 5079 Z= 0.283 Angle : 0.621 5.336 7539 Z= 0.330 Chirality : 0.038 0.232 1016 Planarity : 0.003 0.009 565 Dihedral : 24.055 159.649 2323 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.40), residues: 441 helix: 1.07 (0.45), residues: 143 sheet: -1.53 (1.03), residues: 28 loop : -1.81 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0491 time to fit residues: 1.6188 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.029329 restraints weight = 59181.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.030056 restraints weight = 34202.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.030546 restraints weight = 23947.301| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 5079 Z= 0.430 Angle : 0.794 6.944 7539 Z= 0.421 Chirality : 0.044 0.247 1016 Planarity : 0.004 0.012 565 Dihedral : 24.561 156.254 2323 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 35.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.39), residues: 441 helix: 0.14 (0.43), residues: 136 sheet: -1.79 (0.79), residues: 40 loop : -1.97 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0538 time to fit residues: 1.8182 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 25 optimal weight: 40.0000 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.029653 restraints weight = 57870.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.030392 restraints weight = 32843.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.030918 restraints weight = 22942.256| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 5079 Z= 0.358 Angle : 0.700 5.941 7539 Z= 0.373 Chirality : 0.041 0.232 1016 Planarity : 0.003 0.011 565 Dihedral : 24.278 156.944 2323 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 28.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.39), residues: 441 helix: 0.23 (0.43), residues: 143 sheet: -2.23 (0.89), residues: 33 loop : -1.97 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0480 time to fit residues: 1.5591 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.031013 restraints weight = 56049.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031861 restraints weight = 31848.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032407 restraints weight = 21935.304| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 5079 Z= 0.171 Angle : 0.529 5.096 7539 Z= 0.284 Chirality : 0.035 0.224 1016 Planarity : 0.002 0.008 565 Dihedral : 23.694 159.341 2323 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.42), residues: 441 helix: 1.49 (0.46), residues: 143 sheet: -1.44 (1.04), residues: 28 loop : -1.72 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.365 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0502 time to fit residues: 1.6812 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.029805 restraints weight = 58462.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.030577 restraints weight = 33083.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.031107 restraints weight = 23020.959| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 5079 Z= 0.353 Angle : 0.685 5.795 7539 Z= 0.364 Chirality : 0.040 0.238 1016 Planarity : 0.003 0.010 565 Dihedral : 24.105 156.587 2323 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 28.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.41), residues: 441 helix: 0.94 (0.44), residues: 143 sheet: -1.69 (1.02), residues: 28 loop : -1.82 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1689.45 seconds wall clock time: 31 minutes 21.32 seconds (1881.32 seconds total)