Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:26:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/12_2022/7won_32652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/12_2022/7won_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_32652/12_2022/7won_32652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/12_2022/7won_32652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/12_2022/7won_32652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7won_32652/12_2022/7won_32652.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 Convert atoms to be neutral 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-4807/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 chiralities: 2 Time building chain proxies: 2.43, per 1000 atoms: 0.73 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: 1.28 Conformation dependent library (CDL) restraints added in 489.1 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: 0.18 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: 0.88 Time building geometry restraints manager: 1.41 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 - 19.79: 1792 19.79 - 39.58: 151 39.58 - 59.37: 20 59.37 - 79.16: 3 79.16 - 98.95: 5 Dihedral angle restraints: 1971 sinusoidal: 757 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=" C2 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" C4 NAG A 1 " pdb=" C5 NAG A 1 " ideal model delta sinusoidal sigma weight residual 50.00 -48.95 98.95 1 2.00e+01 2.50e-03 2.77e+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 ... (remaining 1968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 367 0.059 - 0.119: 99 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 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. 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: 8.090 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: 38.080 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.040 Process input model: 16.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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= 0.380 Angle : 0.969 14.217 4620 Z= 0.564 Chirality : 0.060 0.297 492 Planarity : 0.008 0.080 600 Dihedral : 15.098 98.946 1202 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 % 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 *********************** 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 : 0.421 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1806 time to fit residues: 20.2310 Evaluate side-chains 76 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4813 time to fit residues: 1.0457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 487 ASN L 6 GLN L 40 GLN L 91 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 3401 Z= 0.356 Angle : 0.679 8.485 4620 Z= 0.350 Chirality : 0.047 0.191 492 Planarity : 0.005 0.044 600 Dihedral : 8.735 99.486 488 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer Outliers : 6.20 % 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: -4.06 (0.38), residues: 419 helix: -4.50 (0.76), residues: 14 sheet: -2.38 (0.45), residues: 133 loop : -2.90 (0.34), residues: 272 *********************** 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 110 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 99 average time/residue: 0.1958 time to fit residues: 22.6321 Evaluate side-chains 94 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0521 time to fit residues: 1.6155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7180