Starting phenix.real_space_refine on Tue Feb 13 05:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/02_2024/7won_32652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/02_2024/7won_32652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/02_2024/7won_32652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/02_2024/7won_32652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/02_2024/7won_32652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/02_2024/7won_32652.pdb" } resolution = 3.9 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= 0.010 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 2098 2.51 5 N 556 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F GLU 484": "OE1" <-> "OE2" Residue "F GLU 516": "OE1" <-> "OE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.33, per 1000 atoms: 0.70 Number of scatterers: 3318 At special positions: 0 Unit cell: (73.132, 84.024, 80.912, 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 649 8.00 N 556 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 576.7 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 8 sheets defined 1.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.532A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.564A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.501A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 51 removed outlier: 5.896A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.748A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.113A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 102 through 104 66 hydrogen bonds defined for protein. 168 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: 0.78 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 538 1.30 - 1.43: 1004 1.43 - 1.56: 1840 1.56 - 1.69: 0 1.69 - 1.82: 19 Bond restraints: 3401 Sorted by residual: bond pdb=" C ARG H 106 " pdb=" N SER H 107 " ideal model delta sigma weight residual 1.332 1.240 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.19e+01 bond pdb=" CA ASP H 113 " pdb=" C ASP H 113 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.28e-02 6.10e+03 2.98e+01 bond pdb=" CA ARG H 106 " pdb=" C ARG H 106 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.26e-02 6.30e+03 1.35e+01 bond pdb=" CA ARG H 106 " pdb=" CB ARG H 106 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.58e-02 4.01e+03 1.27e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.07: 102 107.07 - 113.80: 1743 113.80 - 120.53: 1324 120.53 - 127.27: 1418 127.27 - 134.00: 33 Bond angle restraints: 4620 Sorted by residual: angle pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" C TYR H 103 " ideal model delta sigma weight residual 109.52 121.19 -11.67 1.55e+00 4.16e-01 5.67e+01 angle pdb=" O VAL H 100 " pdb=" C VAL H 100 " pdb=" N GLN H 101 " ideal model delta sigma weight residual 122.57 114.38 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" N LEU H 112 " pdb=" CA LEU H 112 " pdb=" C LEU H 112 " ideal model delta sigma weight residual 110.35 101.53 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" C ARG H 106 " pdb=" N SER H 107 " pdb=" CA SER H 107 " ideal model delta sigma weight residual 121.54 109.28 12.26 1.91e+00 2.74e-01 4.12e+01 angle pdb=" CA ARG H 106 " pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 120.70 127.27 -6.57 1.03e+00 9.43e-01 4.06e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 1823 20.55 - 41.09: 143 41.09 - 61.64: 19 61.64 - 82.18: 6 82.18 - 102.73: 10 Dihedral angle restraints: 2001 sinusoidal: 787 harmonic: 1214 Sorted by residual: dihedral pdb=" CA PHE F 429 " pdb=" C PHE F 429 " pdb=" N THR F 430 " pdb=" CA THR F 430 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 365 0.059 - 0.119: 101 0.119 - 0.178: 19 0.178 - 0.238: 6 0.238 - 0.297: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASP H 113 " pdb=" N ASP H 113 " pdb=" C ASP H 113 " pdb=" CB ASP H 113 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR H 103 " pdb=" N TYR H 103 " pdb=" C TYR H 103 " pdb=" CB TYR H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 489 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 100 " 0.042 2.00e-02 2.50e+03 7.95e-02 6.33e+01 pdb=" C VAL H 100 " -0.138 2.00e-02 2.50e+03 pdb=" O VAL H 100 " 0.051 2.00e-02 2.50e+03 pdb=" N GLN H 101 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO F 463 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 56 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO L 57 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 50 2.61 - 3.18: 2613 3.18 - 3.75: 4748 3.75 - 4.33: 6402 4.33 - 4.90: 10870 Nonbonded interactions: 24683 Sorted by model distance: nonbonded pdb=" O ARG H 106 " pdb=" C SER H 107 " model vdw 2.035 3.270 nonbonded pdb=" O SER F 371 " pdb=" NH1 ARG H 106 " model vdw 2.238 2.520 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.276 2.440 nonbonded pdb=" O ARG H 106 " pdb=" CA SER H 107 " model vdw 2.278 2.776 nonbonded pdb=" OG SER F 349 " pdb=" O LEU F 452 " model vdw 2.302 2.440 ... (remaining 24678 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=0.00 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: 7.760 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: 38.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.900 Find NCS groups from input model: 0.100 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 : 0.006 0.092 3401 Z= 0.385 Angle : 0.977 14.217 4620 Z= 0.564 Chirality : 0.060 0.297 492 Planarity : 0.008 0.080 600 Dihedral : 16.809 102.726 1232 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.28 % Allowed : 10.14 % Favored : 89.58 % 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: -4.42 (0.35), residues: 419 helix: -4.82 (0.44), residues: 14 sheet: -2.40 (0.44), residues: 127 loop : -3.30 (0.30), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 436 HIS 0.006 0.003 HIS H 35 PHE 0.011 0.002 PHE F 400 TYR 0.021 0.002 TYR H 104 ARG 0.007 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8755 (p0) cc_final: 0.8457 (p0) REVERT: F 474 GLN cc_start: 0.6126 (tp40) cc_final: 0.5872 (tm-30) REVERT: L 16 GLN cc_start: 0.8730 (mm110) cc_final: 0.8170 (mp10) REVERT: H 16 ARG cc_start: 0.2340 (mmt180) cc_final: 0.1977 (mmt180) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1878 time to fit residues: 20.9833 Evaluate side-chains 78 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 106 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN F 474 GLN F 487 ASN L 6 GLN L 16 GLN L 40 GLN L 91 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3401 Z= 0.290 Angle : 0.664 8.528 4620 Z= 0.333 Chirality : 0.046 0.212 492 Planarity : 0.005 0.045 600 Dihedral : 11.853 77.395 522 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 5.92 % Allowed : 17.75 % Favored : 76.34 % 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: -4.02 (0.38), residues: 419 helix: -4.51 (0.76), residues: 14 sheet: -2.37 (0.44), residues: 133 loop : -2.86 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.002 PHE F 338 TYR 0.015 0.002 TYR F 495 ARG 0.006 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8870 (p0) cc_final: 0.8497 (p0) REVERT: F 474 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5864 (tm-30) REVERT: L 6 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8727 (pt0) REVERT: L 16 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8130 (mp10) REVERT: L 34 ASP cc_start: 0.8192 (m-30) cc_final: 0.7909 (m-30) REVERT: L 93 TYR cc_start: 0.8564 (t80) cc_final: 0.8344 (t80) REVERT: H 16 ARG cc_start: 0.2225 (mmt180) cc_final: 0.1916 (mmt180) outliers start: 21 outliers final: 13 residues processed: 103 average time/residue: 0.2065 time to fit residues: 24.7360 Evaluate side-chains 102 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3401 Z= 0.294 Angle : 0.664 9.646 4620 Z= 0.327 Chirality : 0.046 0.244 492 Planarity : 0.005 0.037 600 Dihedral : 10.189 64.217 518 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 5.63 % Allowed : 20.56 % Favored : 73.80 % 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: -3.74 (0.39), residues: 419 helix: -4.55 (0.67), residues: 14 sheet: -2.16 (0.45), residues: 133 loop : -2.66 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.015 0.002 PHE F 338 TYR 0.015 0.002 TYR H 114 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8859 (p0) cc_final: 0.8481 (p0) REVERT: L 16 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8147 (mp10) REVERT: H 16 ARG cc_start: 0.2071 (mmt180) cc_final: 0.1764 (mmt180) REVERT: H 113 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8495 (m-30) outliers start: 20 outliers final: 13 residues processed: 97 average time/residue: 0.1900 time to fit residues: 21.6634 Evaluate side-chains 93 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3401 Z= 0.195 Angle : 0.621 8.167 4620 Z= 0.300 Chirality : 0.046 0.221 492 Planarity : 0.004 0.034 600 Dihedral : 8.476 56.059 518 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 5.63 % Allowed : 20.85 % Favored : 73.52 % 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: -3.49 (0.40), residues: 419 helix: -4.63 (0.66), residues: 14 sheet: -1.95 (0.46), residues: 133 loop : -2.49 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.001 PHE F 338 TYR 0.018 0.001 TYR H 114 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.417 Fit side-chains REVERT: F 354 ASN cc_start: 0.8803 (p0) cc_final: 0.8475 (p0) REVERT: L 16 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8139 (mp10) REVERT: H 16 ARG cc_start: 0.2301 (mmt180) cc_final: 0.0139 (mmt180) REVERT: H 113 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8516 (m-30) outliers start: 20 outliers final: 14 residues processed: 91 average time/residue: 0.1868 time to fit residues: 20.0832 Evaluate side-chains 88 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0030 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN L 40 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3401 Z= 0.224 Angle : 0.633 9.391 4620 Z= 0.308 Chirality : 0.046 0.207 492 Planarity : 0.004 0.031 600 Dihedral : 7.698 56.700 518 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 5.63 % Allowed : 23.66 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.40), residues: 419 helix: -4.69 (0.57), residues: 14 sheet: -1.82 (0.47), residues: 133 loop : -2.40 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.011 0.001 PHE F 338 TYR 0.013 0.001 TYR F 369 ARG 0.003 0.000 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8812 (p0) cc_final: 0.8439 (p0) REVERT: L 16 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8174 (mp10) REVERT: H 16 ARG cc_start: 0.2574 (mmt180) cc_final: 0.0346 (mmt180) REVERT: H 113 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8454 (m-30) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.2011 time to fit residues: 21.7820 Evaluate side-chains 92 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 39 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 23 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3401 Z= 0.148 Angle : 0.602 9.251 4620 Z= 0.290 Chirality : 0.045 0.226 492 Planarity : 0.004 0.032 600 Dihedral : 6.967 58.997 518 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.51 % Allowed : 24.51 % Favored : 70.99 % 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: -3.15 (0.40), residues: 419 helix: -4.93 (0.43), residues: 20 sheet: -1.58 (0.46), residues: 134 loop : -2.22 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.011 0.001 PHE F 456 TYR 0.017 0.001 TYR H 114 ARG 0.003 0.000 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.434 Fit side-chains REVERT: F 354 ASN cc_start: 0.8741 (p0) cc_final: 0.8389 (p0) REVERT: L 16 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8099 (mp10) REVERT: H 16 ARG cc_start: 0.2339 (mmt180) cc_final: -0.0582 (mpt180) REVERT: H 113 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8450 (m-30) outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 0.1961 time to fit residues: 21.7327 Evaluate side-chains 91 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3401 Z= 0.228 Angle : 0.628 8.831 4620 Z= 0.306 Chirality : 0.045 0.231 492 Planarity : 0.004 0.030 600 Dihedral : 6.964 59.376 518 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 5.63 % Allowed : 24.23 % Favored : 70.14 % 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: -3.14 (0.40), residues: 419 helix: -4.95 (0.40), residues: 20 sheet: -1.62 (0.45), residues: 134 loop : -2.18 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.002 PHE F 429 TYR 0.013 0.001 TYR F 369 ARG 0.004 0.000 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.348 Fit side-chains REVERT: F 354 ASN cc_start: 0.8781 (p0) cc_final: 0.8427 (p0) REVERT: L 16 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8102 (mp10) REVERT: H 16 ARG cc_start: 0.2204 (mmt180) cc_final: 0.0047 (mmt180) REVERT: H 113 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8364 (m-30) outliers start: 20 outliers final: 16 residues processed: 90 average time/residue: 0.1869 time to fit residues: 19.9286 Evaluate side-chains 94 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3401 Z= 0.270 Angle : 0.658 9.631 4620 Z= 0.317 Chirality : 0.046 0.230 492 Planarity : 0.004 0.031 600 Dihedral : 7.040 59.890 518 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 5.63 % Allowed : 25.35 % Favored : 69.01 % 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: -3.10 (0.41), residues: 419 helix: -4.92 (0.41), residues: 20 sheet: -1.59 (0.46), residues: 132 loop : -2.16 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 436 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE F 429 TYR 0.019 0.002 TYR H 114 ARG 0.004 0.000 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.397 Fit side-chains REVERT: F 354 ASN cc_start: 0.8782 (p0) cc_final: 0.8428 (p0) REVERT: L 16 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8118 (mp10) REVERT: H 16 ARG cc_start: 0.2290 (mmt180) cc_final: 0.1893 (mmt180) outliers start: 20 outliers final: 19 residues processed: 88 average time/residue: 0.1909 time to fit residues: 19.9081 Evaluate side-chains 96 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.0020 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3401 Z= 0.237 Angle : 0.642 10.178 4620 Z= 0.309 Chirality : 0.045 0.227 492 Planarity : 0.004 0.031 600 Dihedral : 6.951 59.937 518 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 5.92 % Allowed : 25.35 % Favored : 68.73 % 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: -3.04 (0.41), residues: 419 helix: -4.92 (0.41), residues: 20 sheet: -1.50 (0.47), residues: 132 loop : -2.13 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 436 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.002 PHE F 429 TYR 0.015 0.001 TYR H 114 ARG 0.004 0.000 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.392 Fit side-chains REVERT: F 354 ASN cc_start: 0.8773 (p0) cc_final: 0.8411 (p0) REVERT: L 16 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8114 (mp10) REVERT: H 16 ARG cc_start: 0.2237 (mmt180) cc_final: 0.1844 (mmt180) outliers start: 21 outliers final: 19 residues processed: 92 average time/residue: 0.1832 time to fit residues: 19.8903 Evaluate side-chains 99 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3401 Z= 0.184 Angle : 0.622 9.739 4620 Z= 0.297 Chirality : 0.045 0.230 492 Planarity : 0.004 0.031 600 Dihedral : 6.701 59.062 518 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 4.51 % Allowed : 26.76 % Favored : 68.73 % 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: -2.94 (0.41), residues: 419 helix: -4.91 (0.42), residues: 20 sheet: -1.40 (0.47), residues: 132 loop : -2.08 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.010 0.001 PHE F 429 TYR 0.012 0.001 TYR F 369 ARG 0.004 0.000 ARG F 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.392 Fit side-chains REVERT: F 354 ASN cc_start: 0.8741 (p0) cc_final: 0.8388 (p0) REVERT: L 16 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8112 (mp10) REVERT: H 16 ARG cc_start: 0.2508 (mmt180) cc_final: 0.0304 (mmt180) outliers start: 16 outliers final: 16 residues processed: 94 average time/residue: 0.1881 time to fit residues: 20.9238 Evaluate side-chains 97 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN L 55 ASN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110282 restraints weight = 5091.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112392 restraints weight = 3699.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113919 restraints weight = 2971.031| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3401 Z= 0.330 Angle : 0.703 10.055 4620 Z= 0.343 Chirality : 0.047 0.227 492 Planarity : 0.004 0.029 600 Dihedral : 7.153 59.683 518 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 5.07 % Allowed : 26.48 % Favored : 68.45 % 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: -3.03 (0.41), residues: 419 helix: -4.89 (0.41), residues: 20 sheet: -1.54 (0.47), residues: 132 loop : -2.11 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 436 HIS 0.009 0.003 HIS H 35 PHE 0.016 0.002 PHE F 338 TYR 0.015 0.002 TYR H 114 ARG 0.003 0.000 ARG F 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.00 seconds wall clock time: 31 minutes 7.96 seconds (1867.96 seconds total)