Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 18:27:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/10_2023/7e39_30977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/10_2023/7e39_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_30977/10_2023/7e39_30977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/10_2023/7e39_30977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/10_2023/7e39_30977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e39_30977/10_2023/7e39_30977.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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-1.21rc1-5097/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: 2.20, per 1000 atoms: 0.72 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: 1.24 Conformation dependent library (CDL) restraints added in 541.8 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: 0.30 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: 0.71 Time building geometry restraints manager: 1.35 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=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.07e+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 ... (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: 1571 14.32 - 28.63: 182 28.63 - 42.95: 50 42.95 - 57.26: 12 57.26 - 71.58: 7 Dihedral angle restraints: 1822 sinusoidal: 631 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 1819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 310 0.041 - 0.083: 104 0.083 - 0.124: 40 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 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.450 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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= 0.312 Angle : 0.768 8.104 4292 Z= 0.419 Chirality : 0.050 0.207 466 Planarity : 0.005 0.057 562 Dihedral : 14.373 71.576 1051 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 % Allowed : 1.02 % Favored : 98.98 % 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 : 0.394 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1843 time to fit residues: 8.9627 Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4697 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 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: 0.7371 moved from start: 0.0874 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= 0.243 Angle : 0.652 6.618 4292 Z= 0.339 Chirality : 0.048 0.156 466 Planarity : 0.005 0.056 562 Dihedral : 5.772 24.760 450 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.68 % Allowed : 9.18 % Favored : 90.14 % 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: -3.24 (0.39), residues: 406 helix: -3.73 (0.68), residues: 27 sheet: -1.49 (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 35 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.359 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1687 time to fit residues: 6.9799 Evaluate side-chains 34 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0332 time to fit residues: 0.5877 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 35 optimal weight: 40.0000 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3150 Z= 0.135 Angle : 0.552 6.725 4292 Z= 0.285 Chirality : 0.046 0.178 466 Planarity : 0.004 0.063 562 Dihedral : 5.067 24.377 450 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.36 % Allowed : 10.54 % Favored : 88.10 % 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: -2.86 (0.40), residues: 406 helix: -3.27 (0.82), residues: 27 sheet: -1.23 (0.44), residues: 136 loop : -2.21 (0.39), residues: 243 *********************** 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 42 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.368 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 42 average time/residue: 0.1548 time to fit residues: 8.1597 Evaluate side-chains 37 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0331 time to fit residues: 0.5395 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 0.0770 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 overall best weight: 1.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3150 Z= 0.209 Angle : 0.581 8.781 4292 Z= 0.299 Chirality : 0.046 0.156 466 Planarity : 0.004 0.064 562 Dihedral : 5.042 23.060 450 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.70 % Allowed : 13.27 % Favored : 85.03 % 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: -3.35 (0.84), residues: 27 sheet: -1.08 (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 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.396 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.1625 time to fit residues: 7.6910 Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0353 time to fit residues: 0.6653 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.0010 chunk 22 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3150 Z= 0.207 Angle : 0.583 8.201 4292 Z= 0.297 Chirality : 0.046 0.158 466 Planarity : 0.004 0.063 562 Dihedral : 5.048 22.747 450 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.36 % Allowed : 14.97 % Favored : 83.67 % 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: -2.67 (0.40), residues: 406 helix: -3.25 (0.88), residues: 27 sheet: -1.04 (0.45), residues: 135 loop : -2.10 (0.38), residues: 244 *********************** 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 39 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.375 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1768 time to fit residues: 8.4037 Evaluate side-chains 37 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0583 time to fit residues: 0.7649 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1848 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= 0.208 Angle : 0.592 8.679 4292 Z= 0.302 Chirality : 0.046 0.161 466 Planarity : 0.004 0.063 562 Dihedral : 4.994 23.334 450 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.02 % Allowed : 16.67 % Favored : 82.31 % 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: -2.73 (0.40), residues: 406 helix: -3.28 (0.87), residues: 27 sheet: -1.30 (0.42), residues: 149 loop : -2.00 (0.39), residues: 230 *********************** 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: 3 poor density : 37 time to evaluate : 0.365 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1730 time to fit residues: 8.2285 Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0412 time to fit residues: 0.7135 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.0670 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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: 0.7294 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3150 Z= 0.145 Angle : 0.550 8.994 4292 Z= 0.280 Chirality : 0.045 0.168 466 Planarity : 0.004 0.064 562 Dihedral : 4.761 24.877 450 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.36 % Allowed : 16.33 % Favored : 82.31 % 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: -2.57 (0.41), residues: 406 helix: -3.16 (0.86), residues: 27 sheet: -1.24 (0.42), residues: 152 loop : -1.85 (0.40), residues: 227 *********************** 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 41 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 41 average time/residue: 0.1521 time to fit residues: 7.8339 Evaluate side-chains 35 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4689 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.7376 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3150 Z= 0.339 Angle : 0.654 7.632 4292 Z= 0.337 Chirality : 0.048 0.160 466 Planarity : 0.005 0.065 562 Dihedral : 5.275 25.512 450 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.38 % Allowed : 17.01 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.40), residues: 406 helix: -3.24 (0.86), residues: 27 sheet: -1.29 (0.43), residues: 147 loop : -1.97 (0.39), residues: 232 *********************** 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 39 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.1512 time to fit residues: 6.8087 Evaluate side-chains 37 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0386 time to fit residues: 0.8104 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3150 Z= 0.165 Angle : 0.583 8.586 4292 Z= 0.297 Chirality : 0.046 0.177 466 Planarity : 0.004 0.064 562 Dihedral : 4.914 26.925 450 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.02 % Allowed : 17.01 % Favored : 81.97 % 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: -2.51 (0.41), residues: 406 helix: -3.03 (0.88), residues: 27 sheet: -1.29 (0.42), residues: 152 loop : -1.74 (0.41), residues: 227 *********************** 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 : 0.371 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.1435 time to fit residues: 6.6351 Evaluate side-chains 35 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0371 time to fit residues: 0.5300 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.0000 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.7267 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3150 Z= 0.142 Angle : 0.566 8.753 4292 Z= 0.289 Chirality : 0.046 0.167 466 Planarity : 0.004 0.066 562 Dihedral : 4.677 28.077 450 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.68 % Allowed : 17.69 % Favored : 81.63 % 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: -2.27 (0.41), residues: 406 helix: -2.86 (0.91), residues: 27 sheet: -1.07 (0.43), residues: 153 loop : -1.63 (0.40), residues: 226 ********************** 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 39 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.368 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1293 time to fit residues: 6.5707 Evaluate side-chains 34 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0336 time to fit residues: 0.5257 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.073096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066006 restraints weight = 14106.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.067462 restraints weight = 7460.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068386 restraints weight = 4731.029| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3150 Z= 0.139 Angle : 0.568 9.050 4292 Z= 0.291 Chirality : 0.045 0.161 466 Planarity : 0.004 0.062 562 Dihedral : 4.586 27.014 450 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 18.37 % Favored : 81.63 % 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: -2.15 (0.41), residues: 406 helix: -2.84 (0.90), residues: 27 sheet: -1.00 (0.43), residues: 153 loop : -1.52 (0.40), residues: 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1049.52 seconds wall clock time: 19 minutes 33.09 seconds (1173.09 seconds total)