Starting phenix.real_space_refine (version: dev) on Fri Feb 17 17:36:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/02_2023/7r1y_14243.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/02_2023/7r1y_14243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/02_2023/7r1y_14243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/02_2023/7r1y_14243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/02_2023/7r1y_14243.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/02_2023/7r1y_14243.pdb" } resolution = 3.0 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5704 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 689} Chain breaks: 11 Time building chain proxies: 3.59, per 1000 atoms: 0.63 Number of scatterers: 5704 At special positions: 0 Unit cell: (71.9488, 74.752, 122.406, 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 33 16.00 O 1074 8.00 N 982 7.00 C 3615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 829.8 milliseconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 43.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 19 through 37 removed outlier: 3.679A pdb=" N ARG A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.633A pdb=" N GLN A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.522A pdb=" N VAL A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 326 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.781A pdb=" N SER A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 529 through 542 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 647 through 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 689 through 710 Processing helix chain 'A' and resid 761 through 787 Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 797 through 806 removed outlier: 3.605A pdb=" N ILE A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 818 through 834 removed outlier: 3.534A pdb=" N ASP A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 854 through 870 Processing helix chain 'A' and resid 875 through 892 removed outlier: 3.620A pdb=" N LYS A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 881 " --> pdb=" O THR A 877 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.516A pdb=" N VAL A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 927 removed outlier: 3.589A pdb=" N ASP A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.552A pdb=" N CYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.797A pdb=" N TYR A 355 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 376 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 353 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.546A pdb=" N ALA A 446 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.584A pdb=" N GLY A 107 " --> pdb=" O TRP A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 220 removed outlier: 6.627A pdb=" N ALA A 229 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 218 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A 227 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 226 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 271 removed outlier: 3.694A pdb=" N GLN A 267 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 287 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 286 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 303 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 288 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 400 removed outlier: 3.707A pdb=" N ARG A 396 " --> pdb=" O ALA A 407 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 801 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: 1.87 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1895 1.34 - 1.46: 1156 1.46 - 1.58: 2701 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5801 Sorted by residual: bond pdb=" C PRO A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.23e+00 bond pdb=" C VAL A 897 " pdb=" N ASP A 898 " ideal model delta sigma weight residual 1.328 1.340 -0.012 1.30e-02 5.92e+03 9.08e-01 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.29e-01 bond pdb=" C ALA A 229 " pdb=" N GLY A 230 " ideal model delta sigma weight residual 1.331 1.319 0.012 1.46e-02 4.69e+03 6.71e-01 bond pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 1.517 1.524 -0.007 9.30e-03 1.16e+04 6.23e-01 ... (remaining 5796 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.77: 175 106.77 - 113.56: 3243 113.56 - 120.35: 2031 120.35 - 127.14: 2344 127.14 - 133.93: 59 Bond angle restraints: 7852 Sorted by residual: angle pdb=" N ILE A 893 " pdb=" CA ILE A 893 " pdb=" C ILE A 893 " ideal model delta sigma weight residual 113.20 109.80 3.40 9.60e-01 1.09e+00 1.25e+01 angle pdb=" C VAL A 897 " pdb=" N ASP A 898 " pdb=" CA ASP A 898 " ideal model delta sigma weight residual 122.82 127.52 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" C SER A 83 " pdb=" N ILE A 84 " pdb=" CA ILE A 84 " ideal model delta sigma weight residual 122.93 119.05 3.88 1.21e+00 6.83e-01 1.03e+01 angle pdb=" N ASP A 898 " pdb=" CA ASP A 898 " pdb=" C ASP A 898 " ideal model delta sigma weight residual 111.17 115.52 -4.35 1.41e+00 5.03e-01 9.51e+00 angle pdb=" N PRO A 110 " pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 110.70 114.00 -3.30 1.22e+00 6.72e-01 7.33e+00 ... (remaining 7847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3267 17.24 - 34.47: 189 34.47 - 51.71: 80 51.71 - 68.94: 8 68.94 - 86.18: 4 Dihedral angle restraints: 3548 sinusoidal: 1438 harmonic: 2110 Sorted by residual: dihedral pdb=" CA HIS A 349 " pdb=" C HIS A 349 " pdb=" N ALA A 350 " pdb=" CA ALA A 350 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PRO A 468 " pdb=" C PRO A 468 " pdb=" N ILE A 469 " pdb=" CA ILE A 469 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ILE A 469 " pdb=" C ILE A 469 " pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 539 0.027 - 0.054: 225 0.054 - 0.081: 86 0.081 - 0.108: 37 0.108 - 0.135: 24 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CG LEU A 228 " pdb=" CB LEU A 228 " pdb=" CD1 LEU A 228 " pdb=" CD2 LEU A 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 416 " pdb=" N ILE A 416 " pdb=" C ILE A 416 " pdb=" CB ILE A 416 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 908 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 52 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 110 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 111 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 473 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.022 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1103 2.78 - 3.31: 5462 3.31 - 3.84: 9467 3.84 - 4.37: 11138 4.37 - 4.90: 19024 Nonbonded interactions: 46194 Sorted by model distance: nonbonded pdb=" N LEU A 145 " pdb=" O ALA A 168 " model vdw 2.252 2.520 nonbonded pdb=" OG1 THR A 169 " pdb=" O ASP A 172 " model vdw 2.302 2.440 nonbonded pdb=" OE1 GLN A 287 " pdb=" OH TYR A 289 " model vdw 2.334 2.440 nonbonded pdb=" OE1 GLN A 891 " pdb=" OG1 THR A 921 " model vdw 2.353 2.440 nonbonded pdb=" OD2 ASP A 232 " pdb=" OH TYR A 236 " model vdw 2.361 2.440 ... (remaining 46189 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 33 5.16 5 C 3615 2.51 5 N 982 2.21 5 O 1074 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 individual isotropic 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.160 Check model and map are aligned: 0.100 Process input model: 19.040 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.002 0.039 5801 Z= 0.157 Angle : 0.524 8.992 7852 Z= 0.293 Chirality : 0.041 0.135 911 Planarity : 0.004 0.046 1008 Dihedral : 13.126 86.178 2170 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.32), residues: 699 helix: 1.36 (0.31), residues: 286 sheet: -0.03 (0.42), residues: 156 loop : -0.79 (0.38), residues: 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.715 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 128 average time/residue: 0.9204 time to fit residues: 124.6820 Evaluate side-chains 68 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.9833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 477 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 891 GLN ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 5801 Z= 0.241 Angle : 0.598 9.651 7852 Z= 0.308 Chirality : 0.043 0.163 911 Planarity : 0.005 0.039 1008 Dihedral : 4.447 16.206 770 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 6.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.67 (0.32), residues: 699 helix: 1.79 (0.31), residues: 282 sheet: -0.03 (0.43), residues: 148 loop : -0.68 (0.37), residues: 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 67 time to evaluate : 0.766 Fit side-chains outliers start: 42 outliers final: 18 residues processed: 100 average time/residue: 0.8572 time to fit residues: 91.6403 Evaluate side-chains 78 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 3 average time/residue: 0.1271 time to fit residues: 1.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 5801 Z= 0.241 Angle : 0.600 9.366 7852 Z= 0.304 Chirality : 0.043 0.160 911 Planarity : 0.005 0.042 1008 Dihedral : 4.509 16.587 770 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 7.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.55 (0.32), residues: 699 helix: 1.74 (0.31), residues: 286 sheet: -0.07 (0.42), residues: 148 loop : -0.87 (0.37), residues: 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 63 time to evaluate : 0.717 Fit side-chains outliers start: 46 outliers final: 19 residues processed: 101 average time/residue: 0.8526 time to fit residues: 91.9210 Evaluate side-chains 72 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 0.1269 time to fit residues: 1.2826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 0.0000 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5801 Z= 0.166 Angle : 0.576 12.918 7852 Z= 0.284 Chirality : 0.042 0.141 911 Planarity : 0.004 0.040 1008 Dihedral : 4.274 17.220 770 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 7.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.77 (0.32), residues: 699 helix: 1.94 (0.31), residues: 286 sheet: -0.02 (0.42), residues: 148 loop : -0.73 (0.37), residues: 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 57 time to evaluate : 0.728 Fit side-chains outliers start: 46 outliers final: 23 residues processed: 95 average time/residue: 0.8519 time to fit residues: 86.5918 Evaluate side-chains 74 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 51 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.1172 time to fit residues: 1.4853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 5801 Z= 0.292 Angle : 0.623 7.830 7852 Z= 0.321 Chirality : 0.044 0.149 911 Planarity : 0.005 0.043 1008 Dihedral : 4.769 16.584 770 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 6.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.54 (0.32), residues: 699 helix: 1.84 (0.31), residues: 284 sheet: -0.31 (0.41), residues: 159 loop : -0.84 (0.38), residues: 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 62 time to evaluate : 0.722 Fit side-chains outliers start: 44 outliers final: 24 residues processed: 98 average time/residue: 0.8374 time to fit residues: 87.7813 Evaluate side-chains 78 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 54 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.3329 time to fit residues: 2.9142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5801 Z= 0.167 Angle : 0.546 8.053 7852 Z= 0.280 Chirality : 0.041 0.140 911 Planarity : 0.004 0.043 1008 Dihedral : 4.356 16.432 770 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 5.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.80 (0.32), residues: 699 helix: 2.07 (0.32), residues: 285 sheet: -0.17 (0.42), residues: 151 loop : -0.72 (0.37), residues: 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 57 time to evaluate : 0.684 Fit side-chains outliers start: 38 outliers final: 22 residues processed: 89 average time/residue: 0.8703 time to fit residues: 82.8904 Evaluate side-chains 75 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.0766 time to fit residues: 1.2470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5801 Z= 0.173 Angle : 0.569 12.111 7852 Z= 0.283 Chirality : 0.043 0.360 911 Planarity : 0.004 0.039 1008 Dihedral : 4.293 16.734 770 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 6.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.89 (0.33), residues: 699 helix: 2.08 (0.32), residues: 286 sheet: -0.08 (0.42), residues: 151 loop : -0.65 (0.38), residues: 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 53 time to evaluate : 0.698 Fit side-chains outliers start: 40 outliers final: 20 residues processed: 88 average time/residue: 0.8078 time to fit residues: 76.3087 Evaluate side-chains 71 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.1591 time to fit residues: 1.3703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 54 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5801 Z= 0.166 Angle : 0.556 9.753 7852 Z= 0.283 Chirality : 0.043 0.306 911 Planarity : 0.004 0.041 1008 Dihedral : 4.202 16.976 770 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 4.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.90 (0.33), residues: 699 helix: 2.07 (0.32), residues: 286 sheet: -0.03 (0.42), residues: 151 loop : -0.64 (0.38), residues: 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 54 time to evaluate : 0.682 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 78 average time/residue: 0.9114 time to fit residues: 75.7775 Evaluate side-chains 70 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.1475 time to fit residues: 1.3275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5801 Z= 0.197 Angle : 0.579 8.894 7852 Z= 0.297 Chirality : 0.044 0.319 911 Planarity : 0.004 0.039 1008 Dihedral : 4.330 16.881 770 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.85 (0.33), residues: 699 helix: 2.01 (0.32), residues: 286 sheet: 0.02 (0.42), residues: 149 loop : -0.70 (0.38), residues: 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 50 time to evaluate : 0.734 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 74 average time/residue: 0.9432 time to fit residues: 74.3706 Evaluate side-chains 68 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.4713 time to fit residues: 2.4898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5801 Z= 0.174 Angle : 0.558 8.703 7852 Z= 0.283 Chirality : 0.043 0.275 911 Planarity : 0.004 0.041 1008 Dihedral : 4.217 16.482 770 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.92 (0.33), residues: 699 helix: 2.03 (0.32), residues: 286 sheet: 0.04 (0.42), residues: 149 loop : -0.59 (0.39), residues: 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 0.730 Fit side-chains outliers start: 21 outliers final: 20 residues processed: 71 average time/residue: 1.0161 time to fit residues: 76.9126 Evaluate side-chains 65 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.1026 time to fit residues: 1.1196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 0.0370 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.0370 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.173325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.152018 restraints weight = 8996.507| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.92 r_work: 0.3917 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5801 Z= 0.171 Angle : 0.561 8.344 7852 Z= 0.284 Chirality : 0.043 0.270 911 Planarity : 0.004 0.041 1008 Dihedral : 4.170 16.103 770 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.97 (0.33), residues: 699 helix: 2.06 (0.32), residues: 286 sheet: 0.11 (0.42), residues: 149 loop : -0.58 (0.39), residues: 264 =============================================================================== Job complete usr+sys time: 2071.06 seconds wall clock time: 37 minutes 57.26 seconds (2277.26 seconds total)