Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:21:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/11_2022/7lkh_23408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/11_2022/7lkh_23408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/11_2022/7lkh_23408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/11_2022/7lkh_23408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/11_2022/7lkh_23408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/11_2022/7lkh_23408.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4179 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2338 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 22, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.88, per 1000 atoms: 0.69 Number of scatterers: 4179 At special positions: 0 Unit cell: (70.2, 100.44, 88.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 793 8.00 N 717 7.00 C 2661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 667 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 732.1 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 25.6% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.667A pdb=" N ARG A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.925A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.745A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.765A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.711A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.711A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE A 681 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN A 95 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 683 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE A 97 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A 685 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS A 99 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 687 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 101 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.429A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.924A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1333 1.34 - 1.46: 1038 1.46 - 1.58: 1904 1.58 - 1.71: 0 1.71 - 1.83: 9 Bond restraints: 4284 Sorted by residual: bond pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.19e-02 7.06e+03 1.23e+01 bond pdb=" N THR A 59 " pdb=" CA THR A 59 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.19e+01 bond pdb=" N VAL A 61 " pdb=" CA VAL A 61 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 6.85e+00 bond pdb=" N LYS A 62 " pdb=" CA LYS A 62 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.86e+00 bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.31e+00 ... (remaining 4279 not shown) Histogram of bond angle deviations from ideal: 101.21 - 107.78: 212 107.78 - 114.35: 2382 114.35 - 120.91: 1885 120.91 - 127.48: 1286 127.48 - 134.04: 62 Bond angle restraints: 5827 Sorted by residual: angle pdb=" C LEU L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta sigma weight residual 119.84 113.38 6.46 1.25e+00 6.40e-01 2.67e+01 angle pdb=" C ASP A 83 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" CA VAL A 61 " pdb=" C VAL A 61 " pdb=" O VAL A 61 " ideal model delta sigma weight residual 121.59 117.51 4.08 1.03e+00 9.43e-01 1.57e+01 angle pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" O LYS A 62 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.18e+00 7.18e-01 1.45e+01 angle pdb=" CA ARG A 673 " pdb=" C ARG A 673 " pdb=" O ARG A 673 " ideal model delta sigma weight residual 121.60 117.02 4.58 1.21e+00 6.83e-01 1.43e+01 ... (remaining 5822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2324 16.91 - 33.81: 185 33.81 - 50.71: 33 50.71 - 67.62: 4 67.62 - 84.52: 8 Dihedral angle restraints: 2554 sinusoidal: 1040 harmonic: 1514 Sorted by residual: dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 2551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 423 0.042 - 0.084: 139 0.084 - 0.126: 64 0.126 - 0.169: 19 0.169 - 0.211: 3 Chirality restraints: 648 Sorted by residual: chirality pdb=" CA LYS A 256 " pdb=" N LYS A 256 " pdb=" C LYS A 256 " pdb=" CB LYS A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PHE A 65 " pdb=" N PHE A 65 " pdb=" C PHE A 65 " pdb=" CB PHE A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ARG L 53 " pdb=" N ARG L 53 " pdb=" C ARG L 53 " pdb=" CB ARG L 53 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 645 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 40 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO H 41 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.065 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 155 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 65 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 66 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.032 5.00e-02 4.00e+02 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 26 2.50 - 3.10: 3058 3.10 - 3.70: 5794 3.70 - 4.30: 8688 4.30 - 4.90: 14923 Nonbonded interactions: 32489 Sorted by model distance: nonbonded pdb=" O4 NAG B 1 " pdb=" O7 NAG B 2 " model vdw 1.903 2.440 nonbonded pdb=" OD2 ASP H 73 " pdb=" OG SER H 76 " model vdw 2.057 2.440 nonbonded pdb=" O GLY A 87 " pdb=" OH TYR A 674 " model vdw 2.096 2.440 nonbonded pdb=" O ASN L 77 " pdb=" OD1 ASN L 77 " model vdw 2.245 3.040 nonbonded pdb=" O PHE A 276 " pdb=" O ALA A 671 " model vdw 2.276 3.040 ... (remaining 32484 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 2661 2.51 5 N 717 2.21 5 O 793 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.710 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: 4.540 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.030 Process input model: 15.600 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 4284 Z= 0.384 Angle : 0.933 9.116 5827 Z= 0.564 Chirality : 0.054 0.211 648 Planarity : 0.007 0.112 743 Dihedral : 13.203 84.519 1569 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.37), residues: 506 helix: -0.11 (0.59), residues: 80 sheet: -0.14 (0.39), residues: 171 loop : -1.16 (0.39), residues: 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.561 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.1876 time to fit residues: 18.5131 Evaluate side-chains 51 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0548 time to fit residues: 0.7902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 167 HIS ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 37 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4284 Z= 0.195 Angle : 0.659 15.498 5827 Z= 0.329 Chirality : 0.046 0.179 648 Planarity : 0.006 0.072 743 Dihedral : 4.691 21.246 581 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.45 (0.37), residues: 506 helix: 0.34 (0.62), residues: 72 sheet: 0.04 (0.38), residues: 165 loop : -0.63 (0.39), residues: 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.508 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.1367 time to fit residues: 13.0551 Evaluate side-chains 56 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0437 time to fit residues: 1.0052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 176 ASN ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 39 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4284 Z= 0.242 Angle : 0.643 12.129 5827 Z= 0.325 Chirality : 0.046 0.163 648 Planarity : 0.005 0.053 743 Dihedral : 4.513 19.156 581 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.20 (0.38), residues: 506 helix: 0.48 (0.61), residues: 72 sheet: 0.04 (0.39), residues: 167 loop : -0.32 (0.41), residues: 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.495 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.1489 time to fit residues: 14.0923 Evaluate side-chains 57 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0443 time to fit residues: 0.9254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4284 Z= 0.223 Angle : 0.632 12.614 5827 Z= 0.316 Chirality : 0.045 0.156 648 Planarity : 0.005 0.044 743 Dihedral : 4.434 18.625 581 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.08 (0.39), residues: 506 helix: 0.52 (0.60), residues: 74 sheet: 0.05 (0.39), residues: 167 loop : -0.18 (0.42), residues: 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.565 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 69 average time/residue: 0.1518 time to fit residues: 13.6937 Evaluate side-chains 61 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0478 time to fit residues: 1.4497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.180 Angle : 0.594 10.954 5827 Z= 0.296 Chirality : 0.044 0.146 648 Planarity : 0.005 0.042 743 Dihedral : 4.245 17.630 581 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.02 (0.39), residues: 506 helix: 0.44 (0.59), residues: 75 sheet: 0.14 (0.39), residues: 169 loop : -0.13 (0.43), residues: 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.518 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.1439 time to fit residues: 13.1754 Evaluate side-chains 62 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0443 time to fit residues: 0.7931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4284 Z= 0.226 Angle : 0.616 11.680 5827 Z= 0.309 Chirality : 0.045 0.149 648 Planarity : 0.005 0.044 743 Dihedral : 4.305 17.397 581 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.07 (0.39), residues: 506 helix: 0.33 (0.58), residues: 75 sheet: 0.11 (0.39), residues: 169 loop : -0.14 (0.43), residues: 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.426 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.1416 time to fit residues: 13.1660 Evaluate side-chains 71 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0497 time to fit residues: 1.5265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4284 Z= 0.220 Angle : 0.617 10.506 5827 Z= 0.307 Chirality : 0.045 0.146 648 Planarity : 0.004 0.045 743 Dihedral : 4.295 17.084 581 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.14 (0.39), residues: 506 helix: 0.31 (0.58), residues: 75 sheet: 0.10 (0.39), residues: 168 loop : -0.23 (0.43), residues: 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.527 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.1435 time to fit residues: 12.9281 Evaluate side-chains 64 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0409 time to fit residues: 0.9782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.180 Angle : 0.585 11.516 5827 Z= 0.295 Chirality : 0.043 0.141 648 Planarity : 0.004 0.043 743 Dihedral : 4.245 17.202 581 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.08 (0.39), residues: 506 helix: 0.42 (0.58), residues: 75 sheet: 0.11 (0.39), residues: 168 loop : -0.19 (0.43), residues: 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.525 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.1463 time to fit residues: 13.0066 Evaluate side-chains 62 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0614 time to fit residues: 1.0053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4284 Z= 0.228 Angle : 0.626 11.037 5827 Z= 0.313 Chirality : 0.045 0.151 648 Planarity : 0.004 0.045 743 Dihedral : 4.276 17.296 581 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.15 (0.39), residues: 506 helix: 0.29 (0.58), residues: 75 sheet: 0.09 (0.39), residues: 168 loop : -0.23 (0.43), residues: 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.548 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.1416 time to fit residues: 12.0424 Evaluate side-chains 60 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0439 time to fit residues: 0.7952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4284 Z= 0.226 Angle : 0.615 10.241 5827 Z= 0.310 Chirality : 0.044 0.152 648 Planarity : 0.004 0.045 743 Dihedral : 4.315 17.048 581 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.17 (0.39), residues: 506 helix: 0.30 (0.58), residues: 75 sheet: 0.05 (0.40), residues: 168 loop : -0.24 (0.43), residues: 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.508 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1482 time to fit residues: 12.2153 Evaluate side-chains 59 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 0.0170 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131969 restraints weight = 5552.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135577 restraints weight = 3394.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138064 restraints weight = 2478.349| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4284 Z= 0.158 Angle : 0.593 11.107 5827 Z= 0.294 Chirality : 0.043 0.152 648 Planarity : 0.004 0.043 743 Dihedral : 4.145 16.760 581 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.02 (0.39), residues: 506 helix: 0.44 (0.59), residues: 75 sheet: 0.36 (0.41), residues: 161 loop : -0.29 (0.42), residues: 270 =============================================================================== Job complete usr+sys time: 1189.89 seconds wall clock time: 22 minutes 58.86 seconds (1378.86 seconds total)