Starting phenix.real_space_refine on Thu Nov 14 08:00:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/11_2024/8bgu_16036.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/11_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_16036/11_2024/8bgu_16036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/11_2024/8bgu_16036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/11_2024/8bgu_16036.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgu_16036/11_2024/8bgu_16036.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 P 121 5.49 5 C 2457 2.51 5 N 908 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.91, per 1000 atoms: 0.82 Number of scatterers: 4779 At special positions: 0 Unit cell: (78.366, 102.723, 130.257, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 P 121 15.00 O 1292 8.00 N 908 7.00 C 2457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 448.6 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: 2.21 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: 1.80 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 567 1.30 - 1.38: 1132 1.38 - 1.46: 1169 1.46 - 1.54: 1922 1.54 - 1.62: 289 Bond restraints: 5079 Sorted by residual: bond pdb=" C3' G 3 52 " pdb=" O3' G 3 52 " ideal model delta sigma weight residual 1.417 1.442 -0.025 1.50e-02 4.44e+03 2.76e+00 bond pdb=" CA GLY A 87 " pdb=" C GLY A 87 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.35e+00 bond pdb=" C3' C 3 98 " pdb=" O3' C 3 98 " ideal model delta sigma weight residual 1.417 1.439 -0.022 1.50e-02 4.44e+03 2.21e+00 bond pdb=" N GLY A 87 " pdb=" CA GLY A 87 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.77e+00 bond pdb=" N1 C 3 18 " pdb=" C2 C 3 18 " ideal model delta sigma weight residual 1.397 1.420 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 5074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 7188 1.65 - 3.31: 272 3.31 - 4.96: 54 4.96 - 6.62: 18 6.62 - 8.27: 7 Bond angle restraints: 7539 Sorted by residual: angle pdb=" C GLU B 9 " pdb=" N ASN B 10 " pdb=" CA ASN B 10 " ideal model delta sigma weight residual 120.06 127.14 -7.08 1.19e+00 7.06e-01 3.54e+01 angle pdb=" O3' C 3 98 " pdb=" C3' C 3 98 " pdb=" C2' C 3 98 " ideal model delta sigma weight residual 113.70 121.40 -7.70 1.50e+00 4.44e-01 2.63e+01 angle pdb=" O3' G 3 52 " pdb=" C3' G 3 52 " pdb=" C2' G 3 52 " ideal model delta sigma weight residual 113.70 120.98 -7.28 1.50e+00 4.44e-01 2.36e+01 angle pdb=" C3' G 3 52 " pdb=" O3' G 3 52 " pdb=" P U 3 53 " ideal model delta sigma weight residual 120.20 126.68 -6.48 1.50e+00 4.44e-01 1.87e+01 angle pdb=" N GLY A 87 " pdb=" CA GLY A 87 " pdb=" C GLY A 87 " ideal model delta sigma weight residual 111.67 115.60 -3.93 9.20e-01 1.18e+00 1.83e+01 ... (remaining 7534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 2797 32.82 - 65.64: 300 65.64 - 98.46: 45 98.46 - 131.28: 2 131.28 - 164.10: 1 Dihedral angle restraints: 3145 sinusoidal: 1879 harmonic: 1266 Sorted by residual: dihedral pdb=" O4' U 3 121 " pdb=" C1' U 3 121 " pdb=" N1 U 3 121 " pdb=" C2 U 3 121 " ideal model delta sinusoidal sigma weight residual -128.00 36.10 -164.10 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" CA LEU B 94 " pdb=" C LEU B 94 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" C4' C 3 98 " pdb=" C3' C 3 98 " pdb=" O3' C 3 98 " pdb=" P G 3 99 " ideal model delta sinusoidal sigma weight residual 220.00 98.39 121.61 1 3.50e+01 8.16e-04 1.19e+01 ... (remaining 3142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 926 0.069 - 0.138: 87 0.138 - 0.207: 1 0.207 - 0.276: 0 0.276 - 0.345: 2 Chirality restraints: 1016 Sorted by residual: chirality pdb=" C3' C 3 98 " pdb=" C4' C 3 98 " pdb=" O3' C 3 98 " pdb=" C2' C 3 98 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C3' G 3 52 " pdb=" C4' G 3 52 " pdb=" O3' G 3 52 " pdb=" C2' G 3 52 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1' G 3 5 " pdb=" O4' G 3 5 " pdb=" C2' G 3 5 " pdb=" N9 G 3 5 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1013 not shown) Planarity restraints: 565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 3 92 " -0.024 2.00e-02 2.50e+03 1.11e-02 3.40e+00 pdb=" N9 A 3 92 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A 3 92 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 3 92 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A 3 92 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 3 92 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 3 92 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A 3 92 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 3 67 " 0.024 2.00e-02 2.50e+03 1.01e-02 3.05e+00 pdb=" N9 G 3 67 " -0.018 2.00e-02 2.50e+03 pdb=" C8 G 3 67 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G 3 67 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 3 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G 3 67 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G 3 67 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G 3 67 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 3 67 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G 3 67 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G 3 67 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G 3 67 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 191 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ASN A 191 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN A 191 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 192 " 0.010 2.00e-02 2.50e+03 ... (remaining 562 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 909 2.77 - 3.30: 3973 3.30 - 3.83: 9635 3.83 - 4.37: 9745 4.37 - 4.90: 13364 Nonbonded interactions: 37626 Sorted by model distance: nonbonded pdb=" O6 G 3 1 " pdb=" O4 U 3 121 " model vdw 2.235 3.040 nonbonded pdb=" O2' G 3 77 " pdb=" O6 G 3 101 " model vdw 2.323 3.040 nonbonded pdb=" O6 G 3 67 " pdb=" O4 U 3 111 " model vdw 2.329 2.432 nonbonded pdb=" O2 U 3 81 " pdb=" N2 G 3 99 " model vdw 2.333 2.496 nonbonded pdb=" O4 U 3 81 " pdb=" O6 G 3 99 " model vdw 2.379 2.432 ... (remaining 37621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5079 Z= 0.190 Angle : 0.839 8.272 7539 Z= 0.452 Chirality : 0.041 0.345 1016 Planarity : 0.003 0.017 565 Dihedral : 23.471 164.097 2323 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.34), residues: 441 helix: -1.54 (0.31), residues: 142 sheet: -0.77 (0.74), residues: 55 loop : -2.07 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0544 time to fit residues: 1.7443 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 5079 Z= 0.424 Angle : 0.798 6.017 7539 Z= 0.423 Chirality : 0.044 0.248 1016 Planarity : 0.004 0.015 565 Dihedral : 24.363 162.575 2323 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 29.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.39), residues: 441 helix: 0.33 (0.42), residues: 143 sheet: -1.23 (0.68), residues: 54 loop : -1.83 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0500 time to fit residues: 1.7100 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=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: 10.0000 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 40.0000 chunk 49 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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: 0.8572 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 5079 Z= 0.368 Angle : 0.718 6.469 7539 Z= 0.383 Chirality : 0.042 0.232 1016 Planarity : 0.003 0.010 565 Dihedral : 24.498 162.083 2323 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 26.26 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: -1.87 (0.39), residues: 441 helix: 0.14 (0.42), residues: 149 sheet: -1.53 (0.75), residues: 47 loop : -2.15 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0482 time to fit residues: 1.6018 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.0060 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 overall best weight: 6.0008 ------------------------------------------------------------------------------- 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: 0.8565 moved from start: 0.3827 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= 0.305 Angle : 0.639 5.326 7539 Z= 0.339 Chirality : 0.038 0.232 1016 Planarity : 0.003 0.009 565 Dihedral : 24.132 159.506 2323 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.73 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: -1.43 (0.39), residues: 441 helix: 0.78 (0.44), residues: 143 sheet: -1.40 (0.79), residues: 42 loop : -1.99 (0.37), 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 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0572 time to fit residues: 1.8707 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.8556 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 5079 Z= 0.265 Angle : 0.592 5.229 7539 Z= 0.317 Chirality : 0.037 0.228 1016 Planarity : 0.003 0.009 565 Dihedral : 23.948 162.227 2323 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.40), residues: 441 helix: 1.17 (0.45), residues: 143 sheet: -1.23 (1.02), residues: 28 loop : -1.71 (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 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0509 time to fit residues: 1.7363 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 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: 9.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 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: 0.8618 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 5079 Z= 0.497 Angle : 0.869 7.211 7539 Z= 0.458 Chirality : 0.047 0.248 1016 Planarity : 0.004 0.013 565 Dihedral : 24.691 158.041 2323 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 37.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % 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: -0.19 (0.41), residues: 136 sheet: -1.74 (0.77), residues: 40 loop : -2.14 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.371 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0491 time to fit residues: 1.6623 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=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: 20.0000 chunk 29 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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: 0.8564 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 5079 Z= 0.231 Angle : 0.590 5.198 7539 Z= 0.314 Chirality : 0.037 0.226 1016 Planarity : 0.002 0.009 565 Dihedral : 23.996 160.552 2323 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % 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: -1.26 (0.40), residues: 441 helix: 0.94 (0.45), residues: 143 sheet: -1.59 (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 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.528 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0528 time to fit residues: 2.2245 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=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: 4.9990 chunk 26 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 48 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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: 0.8605 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 5079 Z= 0.421 Angle : 0.766 6.411 7539 Z= 0.406 Chirality : 0.043 0.242 1016 Planarity : 0.003 0.011 565 Dihedral : 24.419 158.054 2323 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 33.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.39), residues: 441 helix: 0.15 (0.42), residues: 143 sheet: -1.79 (0.78), residues: 40 loop : -2.03 (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 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0494 time to fit residues: 1.6550 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 40.0000 chunk 29 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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: 0.8603 moved from start: 0.5408 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= 0.390 Angle : 0.736 6.491 7539 Z= 0.391 Chirality : 0.042 0.234 1016 Planarity : 0.003 0.011 565 Dihedral : 24.381 156.795 2323 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % 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: -1.95 (0.39), residues: 441 helix: 0.08 (0.43), residues: 143 sheet: -2.39 (0.87), residues: 33 loop : -2.02 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0421 time to fit residues: 1.4187 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 8.9990 chunk 36 optimal weight: 0.0870 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- 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: 0.8579 moved from start: 0.5219 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= 0.276 Angle : 0.624 5.409 7539 Z= 0.333 Chirality : 0.038 0.229 1016 Planarity : 0.003 0.009 565 Dihedral : 24.045 157.592 2323 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.00 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: -1.41 (0.41), residues: 441 helix: 0.75 (0.45), residues: 143 sheet: -1.86 (0.98), residues: 28 loop : -1.87 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 303 PHE 0.000 0.000 PHE A 113 TYR 0.000 0.000 TYR F 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0612 time to fit residues: 2.0463 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 8.9990 chunk 12 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 0.0020 chunk 31 optimal weight: 0.8980 overall best weight: 5.9798 ------------------------------------------------------------------------------- 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 = 0.2988 r_free = 0.2988 target = 0.042008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.029942 restraints weight = 57276.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030729 restraints weight = 32611.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.031248 restraints weight = 22610.120| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 5079 Z= 0.301 Angle : 0.646 5.528 7539 Z= 0.344 Chirality : 0.039 0.234 1016 Planarity : 0.003 0.010 565 Dihedral : 24.065 156.169 2323 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % 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: -1.37 (0.41), residues: 441 helix: 0.80 (0.44), residues: 143 sheet: -1.46 (1.03), residues: 26 loop : -1.91 (0.38), residues: 272 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: 861.74 seconds wall clock time: 17 minutes 5.65 seconds (1025.65 seconds total)