Starting phenix.real_space_refine on Thu Dec 7 21:12:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/12_2023/8bgu_16036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/12_2023/8bgu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/12_2023/8bgu_16036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/12_2023/8bgu_16036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/12_2023/8bgu_16036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/12_2023/8bgu_16036.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.55, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 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: 2.72 Conformation dependent library (CDL) restraints added in 641.3 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: 2.20 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: 1.73 Time building geometry restraints manager: 2.85 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: 99.91 - 106.58: 703 106.58 - 113.24: 2882 113.24 - 119.91: 1642 119.91 - 126.57: 1971 126.57 - 133.24: 341 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: 2736 32.82 - 65.64: 249 65.64 - 98.46: 45 98.46 - 131.28: 2 131.28 - 164.10: 1 Dihedral angle restraints: 3033 sinusoidal: 1767 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 3030 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 2.440 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 ========== 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: 0.330 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: 1.830 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- 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 : 22.587 164.097 2211 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0546 time to fit residues: 1.7293 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3659 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 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: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 5079 Z= 0.395 Angle : 0.757 6.228 7539 Z= 0.402 Chirality : 0.042 0.193 1016 Planarity : 0.004 0.013 565 Dihedral : 23.569 160.793 2211 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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: -1.40 (0.39), residues: 441 helix: 0.41 (0.42), residues: 143 sheet: -1.12 (0.68), residues: 54 loop : -1.75 (0.39), 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0471 time to fit residues: 1.5495 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5079 Z= 0.279 Angle : 0.607 4.875 7539 Z= 0.326 Chirality : 0.037 0.185 1016 Planarity : 0.003 0.011 565 Dihedral : 23.417 163.223 2211 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % 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: -1.13 (0.40), residues: 441 helix: 0.99 (0.45), residues: 143 sheet: -1.21 (0.78), residues: 42 loop : -1.78 (0.38), residues: 256 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0498 time to fit residues: 1.6920 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 25 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 33 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 47 optimal weight: 0.0050 chunk 14 optimal weight: 10.0000 overall best weight: 6.0406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5079 Z= 0.322 Angle : 0.676 6.106 7539 Z= 0.360 Chirality : 0.040 0.199 1016 Planarity : 0.003 0.011 565 Dihedral : 23.579 160.679 2211 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % 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: -1.28 (0.39), residues: 441 helix: 1.20 (0.45), residues: 137 sheet: -1.30 (0.79), residues: 40 loop : -2.02 (0.36), residues: 264 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0505 time to fit residues: 1.7593 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 5079 Z= 0.336 Angle : 0.664 6.116 7539 Z= 0.355 Chirality : 0.039 0.183 1016 Planarity : 0.003 0.010 565 Dihedral : 23.542 163.384 2211 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 29.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % 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: -1.40 (0.39), residues: 441 helix: 0.75 (0.43), residues: 143 sheet: -1.28 (1.01), residues: 28 loop : -1.94 (0.36), 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 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0483 time to fit residues: 1.6254 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4967 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= 0.380 Angle : 0.724 6.716 7539 Z= 0.386 Chirality : 0.042 0.200 1016 Planarity : 0.003 0.012 565 Dihedral : 23.792 162.788 2211 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 33.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % 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: -1.99 (0.39), residues: 441 helix: 0.03 (0.42), residues: 149 sheet: -1.78 (0.77), residues: 40 loop : -2.17 (0.38), residues: 252 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.545 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0501 time to fit residues: 1.6438 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 5079 Z= 0.118 Angle : 0.479 4.203 7539 Z= 0.257 Chirality : 0.033 0.173 1016 Planarity : 0.002 0.008 565 Dihedral : 22.801 167.725 2211 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: -0.53 (0.42), residues: 441 helix: 1.82 (0.47), residues: 143 sheet: -1.37 (1.05), residues: 28 loop : -1.55 (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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0498 time to fit residues: 1.6642 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 50 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 5079 Z= 0.443 Angle : 0.789 7.240 7539 Z= 0.417 Chirality : 0.044 0.206 1016 Planarity : 0.004 0.012 565 Dihedral : 23.737 163.092 2211 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 38.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % 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: -1.82 (0.38), residues: 441 helix: 0.32 (0.42), residues: 143 sheet: -1.79 (0.78), residues: 40 loop : -2.10 (0.37), 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 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0498 time to fit residues: 1.6754 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4685 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= 0.180 Angle : 0.518 4.404 7539 Z= 0.279 Chirality : 0.035 0.177 1016 Planarity : 0.002 0.008 565 Dihedral : 22.942 167.012 2211 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % 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: -0.78 (0.42), residues: 441 helix: 1.62 (0.47), residues: 143 sheet: -1.57 (1.01), residues: 28 loop : -1.70 (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 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.370 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0502 time to fit residues: 1.7251 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5079 Z= 0.340 Angle : 0.656 5.920 7539 Z= 0.351 Chirality : 0.040 0.193 1016 Planarity : 0.003 0.010 565 Dihedral : 23.364 165.046 2211 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 31.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % 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: -1.33 (0.40), residues: 441 helix: 0.89 (0.44), residues: 150 sheet: -1.70 (1.00), residues: 28 loop : -1.97 (0.38), residues: 263 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0517 time to fit residues: 1.7098 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.042645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.030366 restraints weight = 57209.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031121 restraints weight = 33215.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031672 restraints weight = 23466.555| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5079 Z= 0.278 Angle : 0.598 5.184 7539 Z= 0.321 Chirality : 0.037 0.184 1016 Planarity : 0.003 0.010 565 Dihedral : 23.205 166.166 2211 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 27.39 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: -1.21 (0.41), residues: 441 helix: 1.03 (0.44), residues: 150 sheet: -1.67 (1.01), residues: 28 loop : -1.92 (0.38), residues: 263 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: 787.71 seconds wall clock time: 15 minutes 14.71 seconds (914.71 seconds total)