Sun 23 Dec 22:22:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ifx-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:52 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 168 and 0 Target number of residues in the AU: 168 Target solvent content: 0.6575 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.54 Input MTZ file: 2ifx-4.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 28.919 4.001 Wilson plot Bfac: 82.96 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2192 reflections ( 98.43 % complete ) and 0 restraints for refining 2022 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3217 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2588 (Rfree = 0.000) for 2022 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 0 residues added, 2050 seeds are put forward Round 1: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.421 Round 2: 106 peptides, 13 chains. Longest chain 17 peptides. Score 0.526 Round 3: 111 peptides, 12 chains. Longest chain 14 peptides. Score 0.575 Round 4: 124 peptides, 13 chains. Longest chain 28 peptides. Score 0.613 Round 5: 118 peptides, 13 chains. Longest chain 22 peptides. Score 0.586 Taking the results from Round 4 Chains 13, Residues 111, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3636 restraints for refining 1646 atoms. 3140 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2398 (Rfree = 0.000) for 1646 atoms. Found 5 (7 requested) and removed 11 (3 requested) atoms. Cycle 2: After refmac, R = 0.2237 (Rfree = 0.000) for 1619 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2155 (Rfree = 0.000) for 1604 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2072 (Rfree = 0.000) for 1591 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2040 (Rfree = 0.000) for 1577 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 1629 seeds are put forward NCS extension: 48 residues added (1 deleted due to clashes), 1677 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.296 Round 2: 113 peptides, 18 chains. Longest chain 10 peptides. Score 0.441 Round 3: 127 peptides, 18 chains. Longest chain 16 peptides. Score 0.518 Round 4: 125 peptides, 17 chains. Longest chain 15 peptides. Score 0.530 Round 5: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.439 Taking the results from Round 4 Chains 17, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3757 restraints for refining 1636 atoms. 3342 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2238 (Rfree = 0.000) for 1636 atoms. Found 1 (7 requested) and removed 12 (3 requested) atoms. Cycle 7: After refmac, R = 0.2027 (Rfree = 0.000) for 1603 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.2048 (Rfree = 0.000) for 1586 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.1959 (Rfree = 0.000) for 1572 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1924 (Rfree = 0.000) for 1565 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 1629 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1646 seeds are put forward Round 1: 110 peptides, 19 chains. Longest chain 13 peptides. Score 0.397 Round 2: 126 peptides, 19 chains. Longest chain 13 peptides. Score 0.489 Round 3: 122 peptides, 16 chains. Longest chain 14 peptides. Score 0.538 Round 4: 129 peptides, 19 chains. Longest chain 14 peptides. Score 0.505 Round 5: 115 peptides, 15 chains. Longest chain 14 peptides. Score 0.525 Taking the results from Round 3 Chains 16, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3479 restraints for refining 1563 atoms. 3071 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2002 (Rfree = 0.000) for 1563 atoms. Found 1 (7 requested) and removed 14 (3 requested) atoms. Cycle 12: After refmac, R = 0.2278 (Rfree = 0.000) for 1538 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.1758 (Rfree = 0.000) for 1533 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.1759 (Rfree = 0.000) for 1522 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1718 (Rfree = 0.000) for 1514 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 1576 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1592 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.336 Round 2: 122 peptides, 19 chains. Longest chain 13 peptides. Score 0.467 Round 3: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.441 Round 4: 130 peptides, 19 chains. Longest chain 13 peptides. Score 0.510 Round 5: 123 peptides, 20 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 4 Chains 19, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3725 restraints for refining 1630 atoms. 3300 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1963 (Rfree = 0.000) for 1630 atoms. Found 2 (7 requested) and removed 13 (3 requested) atoms. Cycle 17: After refmac, R = 0.1942 (Rfree = 0.000) for 1615 atoms. Found 0 (7 requested) and removed 9 (3 requested) atoms. Cycle 18: After refmac, R = 0.1775 (Rfree = 0.000) for 1597 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.1723 (Rfree = 0.000) for 1592 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1805 (Rfree = 0.000) for 1589 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 1644 seeds are put forward NCS extension: 0 residues added, 1644 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.315 Round 2: 107 peptides, 18 chains. Longest chain 16 peptides. Score 0.405 Round 3: 111 peptides, 19 chains. Longest chain 14 peptides. Score 0.403 Round 4: 109 peptides, 18 chains. Longest chain 13 peptides. Score 0.417 Round 5: 109 peptides, 16 chains. Longest chain 10 peptides. Score 0.468 Taking the results from Round 5 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3786 restraints for refining 1647 atoms. 3430 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2032 (Rfree = 0.000) for 1647 atoms. Found 1 (7 requested) and removed 11 (3 requested) atoms. Cycle 22: After refmac, R = 0.1922 (Rfree = 0.000) for 1630 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.1871 (Rfree = 0.000) for 1622 atoms. Found 0 (7 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.1828 (Rfree = 0.000) for 1612 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.1816 (Rfree = 0.000) for 1605 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 1640 seeds are put forward NCS extension: 0 residues added, 1640 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 13 peptides. Score 0.276 Round 2: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.322 Round 3: 97 peptides, 17 chains. Longest chain 13 peptides. Score 0.370 Round 4: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.341 Round 5: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.354 Taking the results from Round 3 Chains 17, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3907 restraints for refining 1646 atoms. 3604 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1948 (Rfree = 0.000) for 1646 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 27: After refmac, R = 0.2116 (Rfree = 0.000) for 1638 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 28: After refmac, R = 0.1708 (Rfree = 0.000) for 1632 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.1649 (Rfree = 0.000) for 1625 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1701 (Rfree = 0.000) for 1623 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 1652 seeds are put forward NCS extension: 0 residues added, 1652 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.308 Round 2: 112 peptides, 20 chains. Longest chain 9 peptides. Score 0.383 Round 3: 122 peptides, 20 chains. Longest chain 13 peptides. Score 0.442 Round 4: 113 peptides, 20 chains. Longest chain 9 peptides. Score 0.389 Round 5: 113 peptides, 16 chains. Longest chain 12 peptides. Score 0.490 Taking the results from Round 5 Chains 16, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3842 restraints for refining 1646 atoms. 3470 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1952 (Rfree = 0.000) for 1646 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.2154 (Rfree = 0.000) for 1640 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.1838 (Rfree = 0.000) for 1635 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 34: After refmac, R = 0.1886 (Rfree = 0.000) for 1630 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 35: After refmac, R = 0.1747 (Rfree = 0.000) for 1623 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 1657 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1670 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.254 Round 2: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.314 Round 3: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.377 Round 4: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.303 Round 5: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.336 Taking the results from Round 3 Chains 17, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3897 restraints for refining 1645 atoms. 3590 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1862 (Rfree = 0.000) for 1645 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.1669 (Rfree = 0.000) for 1642 atoms. Found 0 (7 requested) and removed 7 (3 requested) atoms. Cycle 38: After refmac, R = 0.1553 (Rfree = 0.000) for 1633 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1545 (Rfree = 0.000) for 1628 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1464 (Rfree = 0.000) for 1624 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 1663 seeds are put forward NCS extension: 0 residues added, 1663 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.242 Round 2: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.366 Round 3: 92 peptides, 14 chains. Longest chain 12 peptides. Score 0.421 Round 4: 83 peptides, 15 chains. Longest chain 8 peptides. Score 0.336 Round 5: 96 peptides, 15 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 3 Chains 14, Residues 78, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3971 restraints for refining 1647 atoms. 3661 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1846 (Rfree = 0.000) for 1647 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.1743 (Rfree = 0.000) for 1638 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.1617 (Rfree = 0.000) for 1637 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.1483 (Rfree = 0.000) for 1635 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1559 (Rfree = 0.000) for 1631 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 1657 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1672 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.297 Round 2: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.315 Round 3: 77 peptides, 15 chains. Longest chain 7 peptides. Score 0.295 Round 4: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.307 Round 5: 88 peptides, 14 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 74, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2ifx-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2192 reflections ( 98.43 % complete ) and 3870 restraints for refining 1647 atoms. 3573 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1877 (Rfree = 0.000) for 1647 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1850 (Rfree = 0.000) for 1642 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1562 (Rfree = 0.000) for 1639 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1603 (Rfree = 0.000) for 1635 atoms. TimeTaking 29