Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:07:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/11_2022/7e39_30977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/11_2022/7e39_30977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/11_2022/7e39_30977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/11_2022/7e39_30977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/11_2022/7e39_30977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/11_2022/7e39_30977.pdb" } resolution = 3.7 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= 0.002 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 Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ASP 106": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3074 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 705 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.38, per 1000 atoms: 0.77 Number of scatterers: 3074 At special positions: 0 Unit cell: (56.16, 103.68, 76.68, 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 15 16.00 O 588 8.00 N 525 7.00 C 1946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 475.9 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.799A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.173A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.665A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.037A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.613A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 6.210A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.769A pdb=" N MET B 11 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.527A pdb=" N TYR B 49 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.713A pdb=" N VAL C 114 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1003 1.34 - 1.46: 799 1.46 - 1.58: 1330 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3150 Sorted by residual: bond pdb=" CG LEU A 387 " pdb=" CD1 LEU A 387 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.26e-01 bond pdb=" CA PHE A 392 " pdb=" CB PHE A 392 " ideal model delta sigma weight residual 1.536 1.517 0.019 2.08e-02 2.31e+03 8.44e-01 bond pdb=" CG LEU C 45 " pdb=" CD1 LEU C 45 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.06e-01 ... (remaining 3145 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.78: 90 106.78 - 113.61: 1633 113.61 - 120.44: 1166 120.44 - 127.27: 1370 127.27 - 134.10: 33 Bond angle restraints: 4292 Sorted by residual: angle pdb=" N GLY C 111 " pdb=" CA GLY C 111 " pdb=" C GLY C 111 " ideal model delta sigma weight residual 113.18 118.81 -5.63 2.37e+00 1.78e-01 5.65e+00 angle pdb=" CA TYR B 94 " pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 113.90 109.63 4.27 1.80e+00 3.09e-01 5.62e+00 angle pdb=" C GLN B 79 " pdb=" CA GLN B 79 " pdb=" CB GLN B 79 " ideal model delta sigma weight residual 109.26 112.71 -3.45 1.47e+00 4.63e-01 5.51e+00 angle pdb=" C GLY B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.87 117.62 4.25 1.83e+00 2.99e-01 5.38e+00 angle pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sigma weight residual 116.30 124.40 -8.10 3.50e+00 8.16e-02 5.36e+00 ... (remaining 4287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 1577 14.32 - 28.63: 182 28.63 - 42.95: 50 42.95 - 57.26: 12 57.26 - 71.58: 7 Dihedral angle restraints: 1828 sinusoidal: 637 harmonic: 1191 Sorted by residual: dihedral pdb=" CA LEU B 78 " pdb=" C LEU B 78 " pdb=" N GLN B 79 " pdb=" CA GLN B 79 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N GLU B 68 " pdb=" CA GLU B 68 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA GLN B 79 " pdb=" C GLN B 79 " pdb=" N PRO B 80 " pdb=" CA PRO B 80 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 312 0.041 - 0.083: 103 0.083 - 0.124: 39 0.124 - 0.166: 11 0.166 - 0.207: 1 Chirality restraints: 466 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL B 43 " pdb=" N VAL B 43 " pdb=" C VAL B 43 " pdb=" CB VAL B 43 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 463 not shown) Planarity restraints: 563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO B 95 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO B 80 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 456 " 0.004 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE A 456 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 456 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 456 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 456 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 456 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 456 " 0.001 2.00e-02 2.50e+03 ... (remaining 560 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 93 2.68 - 3.24: 3074 3.24 - 3.79: 4685 3.79 - 4.35: 6276 4.35 - 4.90: 10301 Nonbonded interactions: 24429 Sorted by model distance: nonbonded pdb=" NZ LYS B 39 " pdb=" O GLU B 81 " model vdw 2.130 2.520 nonbonded pdb=" OG SER B 63 " pdb=" OG1 THR B 74 " model vdw 2.162 2.440 nonbonded pdb=" NZ LYS B 39 " pdb=" OE2 GLU B 81 " model vdw 2.172 2.520 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.217 2.520 nonbonded pdb=" O TYR B 49 " pdb=" OG SER B 53 " model vdw 2.225 2.440 ... (remaining 24424 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 15 5.16 5 C 1946 2.51 5 N 525 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 5.860 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.005 0.040 3150 Z= 0.305 Angle : 0.762 8.104 4292 Z= 0.417 Chirality : 0.050 0.207 466 Planarity : 0.005 0.057 562 Dihedral : 14.344 71.576 1057 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % 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: -3.52 (0.38), residues: 406 helix: -3.93 (0.60), residues: 33 sheet: -1.59 (0.43), residues: 131 loop : -2.63 (0.36), residues: 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1767 time to fit residues: 8.6038 Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.7410 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 3150 Z= 0.243 Angle : 0.649 6.821 4292 Z= 0.339 Chirality : 0.049 0.227 466 Planarity : 0.005 0.056 562 Dihedral : 5.804 24.746 456 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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: -3.23 (0.39), residues: 406 helix: -3.74 (0.68), residues: 27 sheet: -1.48 (0.43), residues: 131 loop : -2.42 (0.37), residues: 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1645 time to fit residues: 6.7982 Evaluate side-chains 32 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 39 optimal weight: 0.0270 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 40.0000 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3150 Z= 0.132 Angle : 0.554 6.714 4292 Z= 0.287 Chirality : 0.046 0.194 466 Planarity : 0.004 0.064 562 Dihedral : 5.106 24.407 456 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 2.04 % 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: -2.79 (0.40), residues: 406 helix: -3.29 (0.81), residues: 27 sheet: -1.27 (0.43), residues: 143 loop : -2.09 (0.39), residues: 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.392 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.1488 time to fit residues: 7.8568 Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0317 time to fit residues: 0.6495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.7393 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3150 Z= 0.251 Angle : 0.599 8.785 4292 Z= 0.311 Chirality : 0.047 0.214 466 Planarity : 0.005 0.063 562 Dihedral : 5.224 22.695 456 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 1.70 % 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: -2.76 (0.40), residues: 406 helix: -3.39 (0.83), residues: 27 sheet: -1.11 (0.45), residues: 135 loop : -2.14 (0.38), residues: 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.389 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.1366 time to fit residues: 6.5519 Evaluate side-chains 36 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0459 time to fit residues: 0.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 3150 Z= 0.400 Angle : 0.700 8.001 4292 Z= 0.363 Chirality : 0.050 0.252 466 Planarity : 0.005 0.062 562 Dihedral : 5.714 21.805 456 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer Outliers : 2.04 % 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: -2.92 (0.40), residues: 406 helix: -3.63 (0.79), residues: 27 sheet: -1.21 (0.44), residues: 133 loop : -2.24 (0.38), residues: 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.388 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.1433 time to fit residues: 6.4601 Evaluate side-chains 36 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0339 time to fit residues: 0.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7373 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3150 Z= 0.166 Angle : 0.577 9.223 4292 Z= 0.296 Chirality : 0.047 0.215 466 Planarity : 0.004 0.063 562 Dihedral : 5.151 23.007 456 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 2.04 % 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: -2.69 (0.40), residues: 406 helix: -3.42 (0.82), residues: 27 sheet: -1.25 (0.43), residues: 143 loop : -1.96 (0.39), residues: 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.380 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.1355 time to fit residues: 6.5452 Evaluate side-chains 37 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0323 time to fit residues: 0.6183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.7397 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3150 Z= 0.234 Angle : 0.592 8.270 4292 Z= 0.305 Chirality : 0.047 0.220 466 Planarity : 0.005 0.064 562 Dihedral : 5.183 22.188 456 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer Outliers : 2.04 % 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: -2.76 (0.40), residues: 406 helix: -3.34 (0.85), residues: 27 sheet: -1.38 (0.42), residues: 149 loop : -1.96 (0.40), residues: 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.345 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 37 average time/residue: 0.1468 time to fit residues: 6.8543 Evaluate side-chains 32 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0497 time to fit residues: 0.5624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.7398 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 3150 Z= 0.231 Angle : 0.609 8.262 4292 Z= 0.313 Chirality : 0.047 0.218 466 Planarity : 0.004 0.064 562 Dihedral : 5.231 22.991 456 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 1.36 % 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: -2.74 (0.40), residues: 406 helix: -3.34 (0.83), residues: 27 sheet: -1.33 (0.42), residues: 148 loop : -1.97 (0.40), residues: 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.372 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.1592 time to fit residues: 6.8307 Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0333 time to fit residues: 0.6008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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: 0.7354 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3150 Z= 0.150 Angle : 0.561 8.685 4292 Z= 0.287 Chirality : 0.046 0.190 466 Planarity : 0.004 0.065 562 Dihedral : 4.968 25.778 456 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 1.02 % 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: -2.49 (0.41), residues: 406 helix: -3.18 (0.85), residues: 27 sheet: -1.22 (0.43), residues: 146 loop : -1.74 (0.40), residues: 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.331 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 38 average time/residue: 0.1503 time to fit residues: 7.2328 Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.7364 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3150 Z= 0.192 Angle : 0.597 8.180 4292 Z= 0.310 Chirality : 0.046 0.194 466 Planarity : 0.004 0.066 562 Dihedral : 5.040 27.488 456 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.68 % 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: -2.49 (0.41), residues: 406 helix: -3.05 (0.87), residues: 27 sheet: -1.28 (0.42), residues: 152 loop : -1.72 (0.41), residues: 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.376 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.1542 time to fit residues: 7.2177 Evaluate side-chains 36 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0317 time to fit residues: 0.5368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064385 restraints weight = 14170.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065825 restraints weight = 7554.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066772 restraints weight = 4843.827| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3150 Z= 0.166 Angle : 0.596 8.764 4292 Z= 0.309 Chirality : 0.046 0.184 466 Planarity : 0.004 0.066 562 Dihedral : 4.934 27.254 456 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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: -2.43 (0.41), residues: 406 helix: -3.17 (0.74), residues: 33 sheet: -1.24 (0.42), residues: 152 loop : -1.59 (0.42), residues: 221 =============================================================================== Job complete usr+sys time: 996.91 seconds wall clock time: 18 minutes 30.44 seconds (1110.44 seconds total)