Starting phenix.real_space_refine on Thu Dec 7 19:01:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/12_2023/8ck0_16688.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/12_2023/8ck0_16688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/12_2023/8ck0_16688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/12_2023/8ck0_16688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/12_2023/8ck0_16688.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/12_2023/8ck0_16688.pdb" } resolution = 3.8 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= 0.003 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 25 5.16 5 C 2351 2.51 5 N 659 2.21 5 O 727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3762 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3762 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 26, 'TRANS': 451} Chain breaks: 2 Time building chain proxies: 2.48, per 1000 atoms: 0.66 Number of scatterers: 3762 At special positions: 0 Unit cell: (89.1, 94.5, 152.55, 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 25 16.00 O 727 8.00 N 659 7.00 C 2351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 786.6 milliseconds 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 55.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.523A pdb=" N SER A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.553A pdb=" N GLN A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.725A pdb=" N GLY A 281 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 314 through 318 removed outlier: 4.546A pdb=" N LEU A 318 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 364 removed outlier: 4.601A pdb=" N ILE A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.145A pdb=" N THR A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.557A pdb=" N GLY A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 467 removed outlier: 3.569A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 479 through 492 removed outlier: 4.579A pdb=" N ASP A 485 " --> pdb=" O ASP A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 500 through 523 removed outlier: 3.819A pdb=" N ALA A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 3.984A pdb=" N MET A 154 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N CYS A 138 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 163 removed outlier: 9.794A pdb=" N ASP A 170 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 306 214 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.60 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: 1242 1.34 - 1.46: 508 1.46 - 1.57: 2040 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 3836 Sorted by residual: bond pdb=" CA PRO A 426 " pdb=" C PRO A 426 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.25e+01 bond pdb=" C PRO A 426 " pdb=" O PRO A 426 " ideal model delta sigma weight residual 1.246 1.218 0.027 8.50e-03 1.38e+04 1.04e+01 bond pdb=" N ARG A 150 " pdb=" CA ARG A 150 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.35e+00 bond pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.18e-02 7.18e+03 7.50e+00 bond pdb=" N SER A 40 " pdb=" CA SER A 40 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.29e+00 ... (remaining 3831 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.59: 106 105.59 - 112.74: 1987 112.74 - 119.90: 1345 119.90 - 127.06: 1708 127.06 - 134.22: 45 Bond angle restraints: 5191 Sorted by residual: angle pdb=" CA PRO A 426 " pdb=" C PRO A 426 " pdb=" O PRO A 426 " ideal model delta sigma weight residual 120.90 117.93 2.97 7.20e-01 1.93e+00 1.70e+01 angle pdb=" CA LYS A 477 " pdb=" C LYS A 477 " pdb=" O LYS A 477 " ideal model delta sigma weight residual 122.37 118.24 4.13 1.15e+00 7.56e-01 1.29e+01 angle pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" O GLU A 143 " ideal model delta sigma weight residual 121.99 118.00 3.99 1.14e+00 7.69e-01 1.23e+01 angle pdb=" CA ILE A 480 " pdb=" C ILE A 480 " pdb=" O ILE A 480 " ideal model delta sigma weight residual 121.27 117.78 3.49 1.04e+00 9.25e-01 1.13e+01 angle pdb=" CA PRO A 426 " pdb=" C PRO A 426 " pdb=" N PRO A 427 " ideal model delta sigma weight residual 117.73 120.72 -2.99 9.00e-01 1.23e+00 1.10e+01 ... (remaining 5186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2036 17.95 - 35.89: 248 35.89 - 53.84: 55 53.84 - 71.78: 10 71.78 - 89.73: 7 Dihedral angle restraints: 2356 sinusoidal: 965 harmonic: 1391 Sorted by residual: dihedral pdb=" CA ALA A 81 " pdb=" C ALA A 81 " pdb=" N ARG A 82 " pdb=" CA ARG A 82 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA PRO A 80 " pdb=" C PRO A 80 " pdb=" N ALA A 81 " pdb=" CA ALA A 81 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA VAL A 444 " pdb=" C VAL A 444 " pdb=" N MET A 445 " pdb=" CA MET A 445 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 345 0.036 - 0.071: 131 0.071 - 0.107: 55 0.107 - 0.142: 23 0.142 - 0.178: 11 Chirality restraints: 565 Sorted by residual: chirality pdb=" CA LEU A 425 " pdb=" N LEU A 425 " pdb=" C LEU A 425 " pdb=" CB LEU A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA MET A 420 " pdb=" N MET A 420 " pdb=" C MET A 420 " pdb=" CB MET A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 562 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 79 " -0.095 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO A 80 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 416 " -0.025 2.00e-02 2.50e+03 2.55e-02 1.13e+01 pdb=" CG PHE A 416 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 416 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 416 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 416 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 416 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 416 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 84 " 0.014 2.00e-02 2.50e+03 1.55e-02 5.99e+00 pdb=" CG TRP A 84 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 84 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 84 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 84 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 84 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 84 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 84 " 0.001 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 888 2.79 - 3.32: 3797 3.32 - 3.84: 6117 3.84 - 4.37: 6845 4.37 - 4.90: 11622 Nonbonded interactions: 29269 Sorted by model distance: nonbonded pdb=" O GLY A 76 " pdb=" OG SER A 443 " model vdw 2.259 2.440 nonbonded pdb=" NH1 ARG A 402 " pdb=" OE1 GLU A 406 " model vdw 2.286 2.520 nonbonded pdb=" O ASP A 46 " pdb=" OD1 ASP A 46 " model vdw 2.293 3.040 nonbonded pdb=" NH1 ARG A 7 " pdb=" O GLU A 244 " model vdw 2.322 2.520 nonbonded pdb=" OD1 ASP A 144 " pdb=" N LYS A 145 " model vdw 2.323 2.520 ... (remaining 29264 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: 1.100 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: 5.610 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.050 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 0.066 3836 Z= 0.349 Angle : 0.804 9.449 5191 Z= 0.498 Chirality : 0.052 0.178 565 Planarity : 0.007 0.143 684 Dihedral : 16.634 89.728 1458 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 22.71 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.39), residues: 472 helix: 1.61 (0.34), residues: 224 sheet: -0.28 (0.61), residues: 62 loop : -0.47 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 84 HIS 0.003 0.001 HIS A 125 PHE 0.058 0.003 PHE A 416 TYR 0.023 0.002 TYR A 325 ARG 0.005 0.001 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1845 time to fit residues: 28.5873 Evaluate side-chains 119 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3836 Z= 0.289 Angle : 0.627 5.876 5191 Z= 0.325 Chirality : 0.043 0.178 565 Planarity : 0.006 0.068 684 Dihedral : 4.769 27.360 520 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.80 % Allowed : 19.08 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.40), residues: 472 helix: 1.74 (0.33), residues: 233 sheet: 0.23 (0.66), residues: 64 loop : -0.12 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 84 HIS 0.003 0.001 HIS A 34 PHE 0.008 0.002 PHE A 42 TYR 0.015 0.001 TYR A 237 ARG 0.004 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.463 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 133 average time/residue: 0.1488 time to fit residues: 24.4833 Evaluate side-chains 122 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0412 time to fit residues: 1.5758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3836 Z= 0.218 Angle : 0.595 7.545 5191 Z= 0.304 Chirality : 0.042 0.171 565 Planarity : 0.004 0.034 684 Dihedral : 4.701 24.309 520 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.45 % Allowed : 22.95 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.40), residues: 472 helix: 1.82 (0.33), residues: 239 sheet: 0.47 (0.67), residues: 62 loop : -0.09 (0.52), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 84 HIS 0.004 0.001 HIS A 34 PHE 0.009 0.002 PHE A 416 TYR 0.012 0.001 TYR A 237 ARG 0.011 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.454 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 118 average time/residue: 0.1304 time to fit residues: 19.8240 Evaluate side-chains 112 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0405 time to fit residues: 0.8462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 345 ASN A 447 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3836 Z= 0.161 Angle : 0.551 5.708 5191 Z= 0.279 Chirality : 0.041 0.173 565 Planarity : 0.004 0.034 684 Dihedral : 4.534 21.785 520 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.14 % Allowed : 23.19 % Favored : 73.67 % 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: 1.67 (0.40), residues: 472 helix: 2.01 (0.33), residues: 238 sheet: 0.54 (0.65), residues: 62 loop : 0.13 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.008 0.001 PHE A 85 TYR 0.013 0.001 TYR A 237 ARG 0.006 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.395 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 128 average time/residue: 0.1403 time to fit residues: 22.4645 Evaluate side-chains 116 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0500 time to fit residues: 1.2063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3836 Z= 0.329 Angle : 0.629 6.082 5191 Z= 0.326 Chirality : 0.044 0.166 565 Planarity : 0.005 0.039 684 Dihedral : 4.740 22.188 520 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.93 % Allowed : 24.64 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.39), residues: 472 helix: 2.02 (0.33), residues: 239 sheet: 0.39 (0.64), residues: 64 loop : -0.26 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 84 HIS 0.009 0.002 HIS A 125 PHE 0.006 0.002 PHE A 463 TYR 0.011 0.001 TYR A 237 ARG 0.007 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 107 average time/residue: 0.1348 time to fit residues: 18.3058 Evaluate side-chains 109 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0385 time to fit residues: 1.0429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3836 Z= 0.182 Angle : 0.577 7.339 5191 Z= 0.291 Chirality : 0.042 0.169 565 Planarity : 0.004 0.036 684 Dihedral : 4.631 20.021 520 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.21 % Allowed : 24.64 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.39), residues: 472 helix: 2.22 (0.33), residues: 237 sheet: 0.52 (0.63), residues: 64 loop : -0.04 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.009 0.001 PHE A 42 TYR 0.011 0.001 TYR A 237 ARG 0.006 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 112 average time/residue: 0.1322 time to fit residues: 18.8963 Evaluate side-chains 105 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0503 time to fit residues: 0.7750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7781 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3836 Z= 0.157 Angle : 0.574 6.646 5191 Z= 0.288 Chirality : 0.042 0.175 565 Planarity : 0.004 0.034 684 Dihedral : 4.422 17.203 520 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.21 % Allowed : 24.88 % Favored : 73.91 % 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: 2.03 (0.40), residues: 472 helix: 2.45 (0.33), residues: 237 sheet: 0.56 (0.62), residues: 64 loop : 0.12 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 84 HIS 0.004 0.001 HIS A 213 PHE 0.010 0.001 PHE A 42 TYR 0.012 0.001 TYR A 237 ARG 0.005 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.459 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.1360 time to fit residues: 19.5614 Evaluate side-chains 108 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0374 time to fit residues: 0.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 0.0270 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 0.0070 overall best weight: 2.3660 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3836 Z= 0.181 Angle : 0.603 9.279 5191 Z= 0.299 Chirality : 0.041 0.177 565 Planarity : 0.004 0.036 684 Dihedral : 4.346 17.126 520 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.24 % Allowed : 27.54 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.40), residues: 472 helix: 2.49 (0.33), residues: 238 sheet: 0.54 (0.63), residues: 64 loop : 0.20 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.010 0.001 PHE A 42 TYR 0.011 0.001 TYR A 237 ARG 0.004 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.446 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1331 time to fit residues: 18.1489 Evaluate side-chains 100 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3836 Z= 0.162 Angle : 0.617 9.680 5191 Z= 0.302 Chirality : 0.041 0.172 565 Planarity : 0.004 0.035 684 Dihedral : 4.249 16.833 520 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.48 % Allowed : 27.29 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.40), residues: 472 helix: 2.60 (0.33), residues: 238 sheet: 0.67 (0.65), residues: 64 loop : 0.23 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 84 HIS 0.004 0.001 HIS A 213 PHE 0.011 0.001 PHE A 42 TYR 0.011 0.001 TYR A 237 ARG 0.005 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 0.1299 time to fit residues: 17.6951 Evaluate side-chains 108 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0411 time to fit residues: 0.7823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3836 Z= 0.230 Angle : 0.642 9.915 5191 Z= 0.318 Chirality : 0.042 0.168 565 Planarity : 0.004 0.036 684 Dihedral : 4.499 24.400 520 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.48 % Allowed : 27.05 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.40), residues: 472 helix: 2.59 (0.33), residues: 238 sheet: 0.59 (0.65), residues: 64 loop : 0.13 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE A 42 TYR 0.012 0.001 TYR A 237 ARG 0.004 0.000 ARG A 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.1362 time to fit residues: 18.1756 Evaluate side-chains 100 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0386 time to fit residues: 0.7028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 0.0060 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.0050 chunk 27 optimal weight: 3.9990 overall best weight: 1.1214 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.123153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103634 restraints weight = 9103.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106415 restraints weight = 4295.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108261 restraints weight = 2607.362| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3836 Z= 0.174 Angle : 0.642 9.913 5191 Z= 0.310 Chirality : 0.042 0.166 565 Planarity : 0.004 0.034 684 Dihedral : 4.288 18.912 520 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.24 % Allowed : 26.81 % Favored : 72.95 % 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: 2.20 (0.40), residues: 472 helix: 2.62 (0.33), residues: 238 sheet: 0.74 (0.66), residues: 64 loop : 0.10 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 84 HIS 0.004 0.001 HIS A 213 PHE 0.011 0.001 PHE A 42 TYR 0.010 0.001 TYR A 237 ARG 0.003 0.000 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1158.26 seconds wall clock time: 21 minutes 47.53 seconds (1307.53 seconds total)