Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 00:55:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/07_2023/6t6v_10387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/07_2023/6t6v_10387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/07_2023/6t6v_10387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/07_2023/6t6v_10387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/07_2023/6t6v_10387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/07_2023/6t6v_10387_updated.pdb" } resolution = 4.5 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= 0.005 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 2 7.16 5 S 22 5.16 5 C 3881 2.51 5 N 977 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 724": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 5868 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 745, 5864 Unusual residues: {' CA': 1, 'HEM': 2} Classifications: {'peptide': 742, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706, None: 3} Not linked: pdbres="LEU A 743 " pdbres="HEM A 801 " Not linked: pdbres="HEM A 801 " pdbres="HEM A 802 " Not linked: pdbres="HEM A 802 " pdbres=" CA A 803 " Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 745, 5864 Unusual residues: {' CA': 1, 'HEM': 2} Classifications: {'peptide': 742, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706, None: 3} Not linked: pdbres="LEU A 743 " pdbres="HEM A 801 " Not linked: pdbres="HEM A 801 " pdbres="HEM A 802 " Not linked: pdbres="HEM A 802 " pdbres=" CA A 803 " Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 6063 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 2 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 2 " occ=0.50 Time building chain proxies: 6.01, per 1000 atoms: 1.02 Number of scatterers: 5868 At special positions: 0 Unit cell: (79.268, 71.967, 105.343, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 1 19.99 S 22 16.00 O 985 8.00 N 977 7.00 C 3881 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 61.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 3.869A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE A 12 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 83 through 101 removed outlier: 3.817A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.921A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 4.012A pdb=" N HIS A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG A 168 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 170 " --> pdb=" O HIS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 Processing helix chain 'A' and resid 227 through 252 removed outlier: 3.961A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 308 removed outlier: 4.486A pdb=" N LEU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLY A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.551A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 363 through 389 Processing helix chain 'A' and resid 398 through 401 No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 413 through 437 Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 446 through 460 removed outlier: 4.117A pdb=" N LEU A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.945A pdb=" N PHE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.740A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 581 through 584 Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.797A pdb=" N ALA A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.280A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 636 Processing helix chain 'A' and resid 638 through 653 removed outlier: 4.090A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 699 through 702 No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 705 through 708 No H-bonds generated for 'chain 'A' and resid 705 through 708' Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 721 through 741 removed outlier: 4.419A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 849 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: 1.49 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 2618 1.40 - 1.57: 3403 1.57 - 1.75: 0 1.75 - 1.93: 44 1.93 - 2.10: 6 Bond restraints: 6071 Sorted by residual: bond pdb=" C3B HEM A 802 " pdb=" CAB HEM A 802 " ideal model delta sigma weight residual 1.544 1.473 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C3B HEM A 801 " pdb=" CAB HEM A 801 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C HEM A 802 " pdb=" CAC HEM A 802 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CA LEU A 521 " pdb=" C LEU A 521 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.30e-02 5.92e+03 9.88e+00 ... (remaining 6066 not shown) Histogram of bond angle deviations from ideal: 86.03 - 104.43: 125 104.43 - 122.83: 7606 122.83 - 141.23: 591 141.23 - 159.64: 0 159.64 - 178.04: 4 Bond angle restraints: 8326 Sorted by residual: angle pdb=" C VAL A 560 " pdb=" N VAL A 561 " pdb=" CA VAL A 561 " ideal model delta sigma weight residual 120.24 125.28 -5.04 6.30e-01 2.52e+00 6.41e+01 angle pdb=" N GLN A 32 " pdb=" CA GLN A 32 " pdb=" C GLN A 32 " ideal model delta sigma weight residual 113.17 103.47 9.70 1.26e+00 6.30e-01 5.93e+01 angle pdb=" C VAL A 561 " pdb=" CA VAL A 561 " pdb=" CB VAL A 561 " ideal model delta sigma weight residual 114.35 107.17 7.18 1.06e+00 8.90e-01 4.59e+01 angle pdb=" N VAL A 561 " pdb=" CA VAL A 561 " pdb=" C VAL A 561 " ideal model delta sigma weight residual 112.61 122.40 -9.79 1.45e+00 4.76e-01 4.56e+01 angle pdb=" N GLY A 405 " pdb=" CA GLY A 405 " pdb=" C GLY A 405 " ideal model delta sigma weight residual 115.64 124.51 -8.87 1.46e+00 4.69e-01 3.69e+01 ... (remaining 8321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2986 17.44 - 34.87: 282 34.87 - 52.31: 66 52.31 - 69.74: 14 69.74 - 87.18: 10 Dihedral angle restraints: 3358 sinusoidal: 1248 harmonic: 2110 Sorted by residual: dihedral pdb=" C2B HEM A 802 " pdb=" C3B HEM A 802 " pdb=" CAB HEM A 802 " pdb=" CBB HEM A 802 " ideal model delta sinusoidal sigma weight residual 180.00 99.38 80.62 2 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" C2C HEM A 801 " pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " pdb=" CBC HEM A 801 " ideal model delta sinusoidal sigma weight residual 0.00 -61.73 61.73 2 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" C2B HEM A 801 " pdb=" C3B HEM A 801 " pdb=" CAB HEM A 801 " pdb=" CBB HEM A 801 " ideal model delta sinusoidal sigma weight residual 180.00 120.41 59.59 2 1.00e+01 1.00e-02 3.57e+01 ... (remaining 3355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 678 0.077 - 0.154: 156 0.154 - 0.231: 35 0.231 - 0.308: 9 0.308 - 0.386: 5 Chirality restraints: 883 Sorted by residual: chirality pdb=" CB THR A 546 " pdb=" CA THR A 546 " pdb=" OG1 THR A 546 " pdb=" CG2 THR A 546 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA THR A 578 " pdb=" N THR A 578 " pdb=" C THR A 578 " pdb=" CB THR A 578 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB THR A 646 " pdb=" CA THR A 646 " pdb=" OG1 THR A 646 " pdb=" CG2 THR A 646 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 880 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 187 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ARG A 187 " 0.086 2.00e-02 2.50e+03 pdb=" O ARG A 187 " -0.032 2.00e-02 2.50e+03 pdb=" N GLN A 188 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 599 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C TRP A 599 " 0.082 2.00e-02 2.50e+03 pdb=" O TRP A 599 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN A 600 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 286 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C LEU A 286 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU A 286 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE A 287 " 0.027 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 64 2.54 - 3.13: 4491 3.13 - 3.72: 10167 3.72 - 4.31: 13040 4.31 - 4.90: 20628 Nonbonded interactions: 48390 Sorted by model distance: nonbonded pdb=" O GLU A 28 " pdb=" CG GLN A 32 " model vdw 1.944 3.440 nonbonded pdb=" OE1 GLU A 407 " pdb="CA CA A 803 " model vdw 2.047 2.510 nonbonded pdb=" O GLU A 28 " pdb=" CB GLN A 32 " model vdw 2.090 3.440 nonbonded pdb=" NE2 HIS A 331 " pdb="FE HEM A 801 " model vdw 2.125 3.080 nonbonded pdb=" OH TYR A 408 " pdb=" O2A HEM A 802 " model vdw 2.161 2.440 ... (remaining 48385 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=0.50 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: 0.120 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: 1.270 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.530 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.216 6071 Z= 0.613 Angle : 1.341 10.484 8326 Z= 0.759 Chirality : 0.076 0.386 883 Planarity : 0.009 0.051 1040 Dihedral : 15.460 87.178 2018 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.15 % 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: -4.09 (0.25), residues: 741 helix: -2.59 (0.17), residues: 488 sheet: None (None), residues: 0 loop : -2.60 (0.37), residues: 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1656 time to fit residues: 44.1852 Evaluate side-chains 154 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 89 HIS A 217 HIS A 333 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 6071 Z= 0.319 Angle : 0.850 20.731 8326 Z= 0.384 Chirality : 0.045 0.184 883 Planarity : 0.005 0.036 1040 Dihedral : 7.268 78.078 821 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.29), residues: 741 helix: -0.93 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -2.30 (0.38), residues: 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1420 time to fit residues: 35.4493 Evaluate side-chains 147 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 6071 Z= 0.228 Angle : 0.728 12.026 8326 Z= 0.339 Chirality : 0.043 0.212 883 Planarity : 0.004 0.040 1040 Dihedral : 6.978 62.840 821 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.30), residues: 741 helix: -0.24 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -2.07 (0.38), residues: 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1401 time to fit residues: 36.5497 Evaluate side-chains 158 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.0050 chunk 50 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 333 GLN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 672 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 6071 Z= 0.286 Angle : 0.722 8.887 8326 Z= 0.344 Chirality : 0.043 0.178 883 Planarity : 0.004 0.040 1040 Dihedral : 6.835 69.871 821 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.31), residues: 741 helix: 0.09 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -2.05 (0.38), residues: 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1402 time to fit residues: 35.0763 Evaluate side-chains 156 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 333 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 6071 Z= 0.233 Angle : 0.705 7.657 8326 Z= 0.333 Chirality : 0.043 0.203 883 Planarity : 0.004 0.035 1040 Dihedral : 6.626 71.163 821 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.31), residues: 741 helix: 0.34 (0.24), residues: 490 sheet: None (None), residues: 0 loop : -1.73 (0.40), residues: 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.645 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1317 time to fit residues: 33.1555 Evaluate side-chains 154 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 6071 Z= 0.202 Angle : 0.686 6.902 8326 Z= 0.324 Chirality : 0.041 0.183 883 Planarity : 0.004 0.033 1040 Dihedral : 6.484 75.160 821 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.31), residues: 741 helix: 0.41 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -1.72 (0.39), residues: 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.598 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1321 time to fit residues: 33.2831 Evaluate side-chains 153 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 333 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 6071 Z= 0.264 Angle : 0.718 7.068 8326 Z= 0.340 Chirality : 0.042 0.181 883 Planarity : 0.004 0.032 1040 Dihedral : 6.455 71.640 821 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.31), residues: 741 helix: 0.60 (0.24), residues: 483 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1371 time to fit residues: 33.8431 Evaluate side-chains 148 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 6071 Z= 0.298 Angle : 0.745 8.192 8326 Z= 0.349 Chirality : 0.043 0.180 883 Planarity : 0.004 0.034 1040 Dihedral : 6.686 74.822 821 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.31), residues: 741 helix: 0.59 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.615 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1253 time to fit residues: 30.7491 Evaluate side-chains 151 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 6071 Z= 0.255 Angle : 0.740 8.051 8326 Z= 0.349 Chirality : 0.042 0.179 883 Planarity : 0.006 0.169 1040 Dihedral : 6.787 74.993 821 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 741 helix: 0.68 (0.24), residues: 479 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.590 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1265 time to fit residues: 31.1363 Evaluate side-chains 157 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 6071 Z= 0.204 Angle : 0.730 8.543 8326 Z= 0.341 Chirality : 0.042 0.180 883 Planarity : 0.006 0.141 1040 Dihedral : 6.684 76.581 821 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 741 helix: 0.76 (0.24), residues: 481 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1417 time to fit residues: 35.0432 Evaluate side-chains 160 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 60 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.074462 restraints weight = 27487.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078233 restraints weight = 14520.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080934 restraints weight = 9481.998| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 6071 Z= 0.201 Angle : 0.719 8.278 8326 Z= 0.341 Chirality : 0.042 0.180 883 Planarity : 0.005 0.101 1040 Dihedral : 6.667 76.715 821 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.32), residues: 741 helix: 0.68 (0.24), residues: 485 sheet: None (None), residues: 0 loop : -1.40 (0.40), residues: 256 =============================================================================== Job complete usr+sys time: 1436.02 seconds wall clock time: 26 minutes 31.57 seconds (1591.57 seconds total)