Starting phenix.real_space_refine on Sun Mar 10 20:18:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/03_2024/8bgu_16036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/03_2024/8bgu_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_16036/03_2024/8bgu_16036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/03_2024/8bgu_16036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/03_2024/8bgu_16036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/03_2024/8bgu_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-dev-5265/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: 3.70, per 1000 atoms: 0.77 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 670.3 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: 2.23 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: 1.74 Time building geometry restraints manager: 2.88 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: 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 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.880 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.850 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.434 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0744 time to fit residues: 2.2660 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 0.8551 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 5079 Z= 0.411 Angle : 0.778 6.623 7539 Z= 0.412 Chirality : 0.043 0.200 1016 Planarity : 0.004 0.013 565 Dihedral : 24.489 160.857 2323 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 31.06 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: -1.47 (0.38), residues: 441 helix: 0.31 (0.41), residues: 143 sheet: -1.18 (0.68), residues: 54 loop : -1.77 (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 : 0.267 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0396 time to fit residues: 1.3642 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 0.0370 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- 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: 0.8505 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5079 Z= 0.201 Angle : 0.536 4.267 7539 Z= 0.288 Chirality : 0.035 0.179 1016 Planarity : 0.002 0.011 565 Dihedral : 23.937 161.983 2323 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % 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: -0.80 (0.41), residues: 441 helix: 1.28 (0.46), residues: 143 sheet: -1.24 (0.78), residues: 43 loop : -1.54 (0.39), residues: 255 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 : 0.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0481 time to fit residues: 1.6124 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 ------------------------------------------------------------------------------- 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: 20.0000 chunk 37 optimal weight: 40.0000 chunk 25 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 overall best weight: 12.1196 ------------------------------------------------------------------------------- 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: 0.8618 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 5079 Z= 0.599 Angle : 0.967 7.415 7539 Z= 0.511 Chirality : 0.052 0.226 1016 Planarity : 0.005 0.016 565 Dihedral : 24.994 158.127 2323 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 46.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % 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: -2.87 (0.35), residues: 441 helix: -0.88 (0.38), residues: 155 sheet: -1.95 (0.67), residues: 49 loop : -2.69 (0.35), residues: 237 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: 0.0511 time to fit residues: 1.7299 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 ------------------------------------------------------------------------------- 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: 20.0000 chunk 30 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.8566 moved from start: 0.3954 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= 0.302 Angle : 0.647 5.617 7539 Z= 0.345 Chirality : 0.039 0.202 1016 Planarity : 0.003 0.010 565 Dihedral : 24.432 160.719 2323 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 25.69 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: -1.91 (0.38), residues: 441 helix: 0.25 (0.43), residues: 143 sheet: -1.78 (0.95), residues: 30 loop : -2.18 (0.35), residues: 268 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 : 0.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0482 time to fit residues: 1.5785 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 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: 20.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- 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: 0.8615 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.034 5079 Z= 0.499 Angle : 0.880 8.011 7539 Z= 0.467 Chirality : 0.047 0.217 1016 Planarity : 0.004 0.014 565 Dihedral : 25.114 158.563 2323 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 43.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % 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: -2.75 (0.36), residues: 441 helix: -0.68 (0.41), residues: 142 sheet: -2.01 (0.74), residues: 40 loop : -2.59 (0.35), 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 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 : 0.357 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0474 time to fit residues: 1.5909 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 30.0000 chunk 38 optimal weight: 0.0000 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.1790 ------------------------------------------------------------------------------- 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: 0.8538 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5079 Z= 0.176 Angle : 0.540 4.721 7539 Z= 0.288 Chirality : 0.035 0.198 1016 Planarity : 0.002 0.008 565 Dihedral : 24.001 162.584 2323 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.06 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: -1.42 (0.40), residues: 441 helix: 0.97 (0.45), residues: 143 sheet: -1.62 (0.99), residues: 28 loop : -2.06 (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 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 : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0506 time to fit residues: 1.6461 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 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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: 0.8594 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 5079 Z= 0.397 Angle : 0.735 6.911 7539 Z= 0.391 Chirality : 0.043 0.211 1016 Planarity : 0.003 0.011 565 Dihedral : 24.653 159.501 2323 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 35.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % 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: -2.14 (0.38), residues: 441 helix: 0.16 (0.43), residues: 143 sheet: -1.90 (0.77), residues: 40 loop : -2.39 (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 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 : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0425 time to fit residues: 1.4403 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 ------------------------------------------------------------------------------- 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: 30.0000 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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: 0.8529 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5079 Z= 0.154 Angle : 0.507 4.230 7539 Z= 0.271 Chirality : 0.034 0.194 1016 Planarity : 0.002 0.008 565 Dihedral : 23.837 162.610 2323 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % 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: -0.94 (0.41), residues: 441 helix: 1.56 (0.46), residues: 143 sheet: -1.58 (1.00), residues: 28 loop : -1.85 (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 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 : 0.332 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0484 time to fit residues: 1.6047 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 20.0000 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 overall best weight: 6.7590 ------------------------------------------------------------------------------- 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: 0.8578 moved from start: 0.4951 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 : 0.659 6.058 7539 Z= 0.351 Chirality : 0.040 0.206 1016 Planarity : 0.003 0.010 565 Dihedral : 24.295 159.401 2323 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 31.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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: -1.41 (0.40), residues: 441 helix: 1.00 (0.44), residues: 143 sheet: -1.68 (0.78), residues: 40 loop : -2.06 (0.38), 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 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 : 0.316 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0504 time to fit residues: 1.6603 Evaluate side-chains 13 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 50.0000 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 3.1562 ------------------------------------------------------------------------------- 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 = 0.3040 r_free = 0.3040 target = 0.043706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031224 restraints weight = 55308.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.032022 restraints weight = 32191.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032552 restraints weight = 22701.969| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5079 Z= 0.170 Angle : 0.509 4.374 7539 Z= 0.272 Chirality : 0.034 0.180 1016 Planarity : 0.002 0.008 565 Dihedral : 23.780 162.080 2323 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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: -0.76 (0.42), residues: 441 helix: 1.75 (0.47), residues: 143 sheet: -1.66 (0.99), residues: 28 loop : -1.75 (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: 787.98 seconds wall clock time: 15 minutes 18.85 seconds (918.85 seconds total)