Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:26:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/11_2022/7bc7_12141_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/11_2022/7bc7_12141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/11_2022/7bc7_12141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/11_2022/7bc7_12141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/11_2022/7bc7_12141_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/11_2022/7bc7_12141_updated.pdb" } resolution = 3.3 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= 0.053 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4209 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3269 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 17, 'TRANS': 414} Chain: "B" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 909 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LYA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.11, per 1000 atoms: 0.74 Number of scatterers: 4209 At special positions: 0 Unit cell: (104.832, 64.896, 66.56, 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 22 16.00 O 753 8.00 N 700 7.00 C 2734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 620.0 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 3 sheets defined 59.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 30 through 59 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 81 through 119 removed outlier: 3.921A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.858A pdb=" N SER A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 145 Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 185 through 210 removed outlier: 3.920A pdb=" N GLN A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 236 removed outlier: 3.806A pdb=" N LEU A 236 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 removed outlier: 4.111A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 removed outlier: 3.945A pdb=" N LEU A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 335 removed outlier: 3.759A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A 324 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 358 removed outlier: 4.042A pdb=" N ALA A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 376 through 390 removed outlier: 4.051A pdb=" N ALA A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR A 380 " --> pdb=" O MET A 377 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 396 through 424 Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.821A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.801A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 82 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.778A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 92 through 94 251 hydrogen bonds defined for protein. 645 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: 1.12 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 657 1.31 - 1.43: 1206 1.43 - 1.56: 2415 1.56 - 1.68: 0 1.68 - 1.81: 33 Bond restraints: 4311 Sorted by residual: bond pdb=" C20 LYA A 501 " pdb=" N22 LYA A 501 " ideal model delta sigma weight residual 1.340 1.468 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C17 LYA A 501 " pdb=" N19 LYA A 501 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C13 LYA A 501 " pdb=" C14 LYA A 501 " ideal model delta sigma weight residual 1.444 1.367 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta sigma weight residual 1.462 1.494 -0.032 9.50e-03 1.11e+04 1.16e+01 bond pdb=" C13 LYA A 501 " pdb=" C9 LYA A 501 " ideal model delta sigma weight residual 1.434 1.366 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 4306 not shown) Histogram of bond angle deviations from ideal: 97.36 - 106.17: 98 106.17 - 114.97: 2584 114.97 - 123.77: 3065 123.77 - 132.58: 112 132.58 - 141.38: 14 Bond angle restraints: 5873 Sorted by residual: angle pdb=" C10 LYA A 501 " pdb=" C9 LYA A 501 " pdb=" C8 LYA A 501 " ideal model delta sigma weight residual 126.87 110.82 16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C13 LYA A 501 " pdb=" C9 LYA A 501 " pdb=" C8 LYA A 501 " ideal model delta sigma weight residual 126.91 141.38 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N18 LYA A 501 " pdb=" C17 LYA A 501 " pdb=" N19 LYA A 501 " ideal model delta sigma weight residual 116.30 129.65 -13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA VAL A 382 " pdb=" C VAL A 382 " pdb=" O VAL A 382 " ideal model delta sigma weight residual 121.27 117.50 3.77 1.04e+00 9.25e-01 1.31e+01 angle pdb=" N LEU A 387 " pdb=" CA LEU A 387 " pdb=" C LEU A 387 " ideal model delta sigma weight residual 111.28 107.84 3.44 1.09e+00 8.42e-01 9.95e+00 ... (remaining 5868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 2195 17.17 - 34.34: 255 34.34 - 51.51: 34 51.51 - 68.68: 5 68.68 - 85.85: 8 Dihedral angle restraints: 2497 sinusoidal: 932 harmonic: 1565 Sorted by residual: dihedral pdb=" CA GLU A 267 " pdb=" C GLU A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CB CYS A 72 " pdb=" SG CYS A 72 " pdb=" SG CYS A 306 " pdb=" CB CYS A 306 " ideal model delta sinusoidal sigma weight residual 93.00 130.28 -37.28 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA TYR B 80 " pdb=" C TYR B 80 " pdb=" N LEU B 81 " pdb=" CA LEU B 81 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 2494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 398 0.041 - 0.082: 194 0.082 - 0.124: 64 0.124 - 0.165: 13 0.165 - 0.206: 3 Chirality restraints: 672 Sorted by residual: chirality pdb=" C23 LYA A 501 " pdb=" C24 LYA A 501 " pdb=" C29 LYA A 501 " pdb=" N22 LYA A 501 " both_signs ideal model delta sigma weight residual False -2.46 -2.67 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR A 363 " pdb=" N THR A 363 " pdb=" C THR A 363 " pdb=" CB THR A 363 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA LEU A 387 " pdb=" N LEU A 387 " pdb=" C LEU A 387 " pdb=" CB LEU A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 669 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 216 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C TYR A 216 " -0.031 2.00e-02 2.50e+03 pdb=" O TYR A 216 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 217 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 432 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 433 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 433 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 433 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 443 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 444 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.022 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 81 2.67 - 3.23: 4264 3.23 - 3.78: 6614 3.78 - 4.34: 8876 4.34 - 4.90: 14986 Nonbonded interactions: 34821 Sorted by model distance: nonbonded pdb=" O LYS A 249 " pdb=" OG1 THR A 252 " model vdw 2.110 2.440 nonbonded pdb=" O TYR A 299 " pdb=" NH2 ARG A 430 " model vdw 2.233 2.520 nonbonded pdb=" NH1 ARG A 156 " pdb=" OD2 ASP A 164 " model vdw 2.268 2.520 nonbonded pdb=" O SER A 28 " pdb=" OH TYR A 233 " model vdw 2.274 2.440 nonbonded pdb=" O GLY A 113 " pdb=" OG SER A 116 " model vdw 2.282 2.440 ... (remaining 34816 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 22 5.16 5 C 2734 2.51 5 N 700 2.21 5 O 753 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: 1.550 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: 7.570 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.009 0.128 4311 Z= 0.583 Angle : 0.978 16.055 5873 Z= 0.493 Chirality : 0.053 0.206 672 Planarity : 0.005 0.039 733 Dihedral : 14.708 85.854 1499 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.36 % Favored : 90.46 % Rotamer Outliers : 0.23 % 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: -1.48 (0.36), residues: 545 helix: 0.54 (0.29), residues: 325 sheet: -3.74 (0.63), residues: 54 loop : -3.06 (0.44), residues: 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.504 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1319 time to fit residues: 17.9918 Evaluate side-chains 89 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4311 Z= 0.227 Angle : 0.665 8.552 5873 Z= 0.327 Chirality : 0.041 0.153 672 Planarity : 0.005 0.043 733 Dihedral : 6.918 88.496 604 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.92 % 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: -0.90 (0.37), residues: 545 helix: 0.81 (0.29), residues: 335 sheet: -3.60 (0.73), residues: 40 loop : -2.71 (0.45), residues: 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.443 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.1248 time to fit residues: 16.9628 Evaluate side-chains 90 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0476 time to fit residues: 1.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4311 Z= 0.245 Angle : 0.639 8.808 5873 Z= 0.311 Chirality : 0.041 0.153 672 Planarity : 0.005 0.041 733 Dihedral : 6.777 88.801 604 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.60 % 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: -0.81 (0.37), residues: 545 helix: 0.86 (0.29), residues: 335 sheet: -3.46 (0.70), residues: 39 loop : -2.63 (0.44), residues: 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.468 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 0.1280 time to fit residues: 16.5167 Evaluate side-chains 90 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0459 time to fit residues: 0.9585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4311 Z= 0.196 Angle : 0.605 8.381 5873 Z= 0.293 Chirality : 0.040 0.146 672 Planarity : 0.005 0.043 733 Dihedral : 6.558 89.112 604 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.83 % 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: -0.52 (0.37), residues: 545 helix: 1.05 (0.29), residues: 333 sheet: -3.24 (0.70), residues: 39 loop : -2.42 (0.44), residues: 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.475 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 102 average time/residue: 0.1410 time to fit residues: 18.7782 Evaluate side-chains 94 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.480 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0463 time to fit residues: 0.8762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4311 Z= 0.203 Angle : 0.614 8.732 5873 Z= 0.294 Chirality : 0.040 0.153 672 Planarity : 0.005 0.045 733 Dihedral : 6.447 88.273 604 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.37 % 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: -0.33 (0.37), residues: 545 helix: 1.13 (0.29), residues: 333 sheet: -2.53 (0.67), residues: 49 loop : -2.31 (0.46), residues: 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.390 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.1465 time to fit residues: 18.0333 Evaluate side-chains 95 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0443 time to fit residues: 1.0607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4311 Z= 0.221 Angle : 0.624 8.683 5873 Z= 0.299 Chirality : 0.040 0.155 672 Planarity : 0.005 0.042 733 Dihedral : 6.423 88.260 604 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.92 % 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: -0.31 (0.37), residues: 545 helix: 1.15 (0.29), residues: 333 sheet: -2.48 (0.67), residues: 49 loop : -2.32 (0.45), residues: 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.499 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 95 average time/residue: 0.1497 time to fit residues: 18.4168 Evaluate side-chains 93 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0439 time to fit residues: 0.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4311 Z= 0.213 Angle : 0.619 7.516 5873 Z= 0.298 Chirality : 0.040 0.151 672 Planarity : 0.005 0.043 733 Dihedral : 6.406 88.164 604 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.60 % 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: -0.28 (0.37), residues: 545 helix: 1.18 (0.29), residues: 333 sheet: -2.34 (0.68), residues: 49 loop : -2.36 (0.45), residues: 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.490 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 101 average time/residue: 0.1472 time to fit residues: 19.2233 Evaluate side-chains 96 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0477 time to fit residues: 1.0820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4311 Z= 0.218 Angle : 0.628 7.623 5873 Z= 0.302 Chirality : 0.041 0.152 672 Planarity : 0.005 0.043 733 Dihedral : 6.419 88.342 604 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.92 % 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: -0.23 (0.37), residues: 545 helix: 1.21 (0.29), residues: 333 sheet: -2.26 (0.70), residues: 49 loop : -2.36 (0.45), residues: 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.362 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.1284 time to fit residues: 16.6038 Evaluate side-chains 96 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0567 time to fit residues: 1.0224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 0.0370 chunk 53 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 overall best weight: 0.0612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 4311 Z= 0.150 Angle : 0.619 13.577 5873 Z= 0.290 Chirality : 0.039 0.149 672 Planarity : 0.004 0.046 733 Dihedral : 6.156 87.267 604 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 0.07 (0.37), residues: 545 helix: 1.45 (0.30), residues: 330 sheet: -2.79 (0.64), residues: 46 loop : -1.94 (0.45), residues: 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.523 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1647 time to fit residues: 19.3662 Evaluate side-chains 87 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 39 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4311 Z= 0.194 Angle : 0.640 11.718 5873 Z= 0.305 Chirality : 0.041 0.167 672 Planarity : 0.004 0.044 733 Dihedral : 6.332 89.556 604 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.23 % 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 (0.37), residues: 545 helix: 1.35 (0.29), residues: 333 sheet: -1.88 (0.70), residues: 49 loop : -2.08 (0.45), residues: 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.462 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1591 time to fit residues: 19.0829 Evaluate side-chains 94 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0427 time to fit residues: 0.6856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3518 r_free = 0.3518 target = 0.129997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121535 restraints weight = 5795.252| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3400 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 1.51 restraints_weight: 0.2500 r_work: 0.3379 rms_B_bonded: 1.56 restraints_weight: 0.1250 r_work: 0.3368 rms_B_bonded: 1.66 restraints_weight: 0.0625 r_work: 0.3355 rms_B_bonded: 1.79 restraints_weight: 0.0312 r_work: 0.3342 rms_B_bonded: 1.96 restraints_weight: 0.0156 r_work: 0.3328 rms_B_bonded: 2.16 restraints_weight: 0.0078 r_work: 0.3312 rms_B_bonded: 2.40 restraints_weight: 0.0039 r_work: 0.3294 rms_B_bonded: 2.69 restraints_weight: 0.0020 r_work: 0.3275 rms_B_bonded: 3.01 restraints_weight: 0.0010 r_work: 0.3253 rms_B_bonded: 3.39 restraints_weight: 0.0005 r_work: 0.3229 rms_B_bonded: 3.82 restraints_weight: 0.0002 r_work: 0.3203 rms_B_bonded: 4.32 restraints_weight: 0.0001 r_work: 0.3173 rms_B_bonded: 4.89 restraints_weight: 0.0001 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4311 Z= 0.203 Angle : 0.637 11.601 5873 Z= 0.305 Chirality : 0.041 0.165 672 Planarity : 0.005 0.044 733 Dihedral : 6.394 89.963 604 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.46 % 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 (0.37), residues: 545 helix: 1.39 (0.30), residues: 331 sheet: -1.90 (0.71), residues: 49 loop : -2.11 (0.44), residues: 165 =============================================================================== Job complete usr+sys time: 1242.37 seconds wall clock time: 23 minutes 20.24 seconds (1400.24 seconds total)