Sun 23 Dec 22:23:05 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 2etj-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.2-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/2etj-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.2-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 22:23:15 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/2etj-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.2-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 164 and 0 Target number of residues in the AU: 164 Target solvent content: 0.6248 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 250 Adjusted target solvent content: 0.43 Input MTZ file: 2etj-3.2-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: 144 Cell parameters: 51.821 51.821 76.293 90.000 90.000 120.000 Input sequence file: 2etj-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2000 target number of atoms Had to go as low as 0.60 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 Loops will be built when appropriate and at the last cycle Resolution range: 24.534 3.201 Wilson plot Bfac: 63.21 3746 reflections ( 99.76 % complete ) and 0 restraints for refining 2215 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3369 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3085 (Rfree = 0.000) for 2215 atoms. Found 15 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.48 Search for helices and strands: 0 residues in 0 chains, 2253 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.228 Round 2: 94 peptides, 19 chains. Longest chain 7 peptides. Score 0.307 Round 3: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.357 Round 4: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.418 Round 5: 126 peptides, 20 chains. Longest chain 24 peptides. Score 0.491 Taking the results from Round 5 Chains 21, Residues 106, Estimated correctness of the model 8.3 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3945 restraints for refining 1785 atoms. 3498 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2467 (Rfree = 0.000) for 1785 atoms. Found 11 (16 requested) and removed 27 (8 requested) atoms. Cycle 2: After refmac, R = 0.2642 (Rfree = 0.000) for 1736 atoms. Found 14 (15 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2045 (Rfree = 0.000) for 1712 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.2112 (Rfree = 0.000) for 1699 atoms. Found 3 (15 requested) and removed 19 (7 requested) atoms. Cycle 5: After refmac, R = 0.2831 (Rfree = 0.000) for 1674 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 1750 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 13 peptides. Score 0.355 Round 2: 119 peptides, 20 chains. Longest chain 19 peptides. Score 0.448 Round 3: 123 peptides, 17 chains. Longest chain 17 peptides. Score 0.549 Round 4: 128 peptides, 17 chains. Longest chain 19 peptides. Score 0.576 Round 5: 130 peptides, 20 chains. Longest chain 13 peptides. Score 0.514 Taking the results from Round 4 Chains 17, Residues 111, Estimated correctness of the model 34.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3881 restraints for refining 1696 atoms. 3454 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2862 (Rfree = 0.000) for 1696 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 7: After refmac, R = 0.2578 (Rfree = 0.000) for 1669 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 8: After refmac, R = 0.2601 (Rfree = 0.000) for 1652 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.2594 (Rfree = 0.000) for 1641 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.2533 (Rfree = 0.000) for 1632 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 1718 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 10 peptides. Score 0.289 Round 2: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.420 Round 3: 125 peptides, 20 chains. Longest chain 14 peptides. Score 0.485 Round 4: 110 peptides, 15 chains. Longest chain 16 peptides. Score 0.526 Round 5: 117 peptides, 18 chains. Longest chain 17 peptides. Score 0.489 Taking the results from Round 4 Chains 15, Residues 95, Estimated correctness of the model 19.5 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3611 restraints for refining 1676 atoms. 3210 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2109 (Rfree = 0.000) for 1676 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.1888 (Rfree = 0.000) for 1670 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.1892 (Rfree = 0.000) for 1664 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.2054 (Rfree = 0.000) for 1658 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.1734 (Rfree = 0.000) for 1656 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 1689 seeds are put forward Round 1: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.368 Round 2: 116 peptides, 18 chains. Longest chain 9 peptides. Score 0.483 Round 3: 119 peptides, 20 chains. Longest chain 9 peptides. Score 0.448 Round 4: 113 peptides, 18 chains. Longest chain 10 peptides. Score 0.465 Round 5: 107 peptides, 18 chains. Longest chain 8 peptides. Score 0.426 Taking the results from Round 2 Chains 18, Residues 98, Estimated correctness of the model 5.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3629 restraints for refining 1655 atoms. 3255 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2215 (Rfree = 0.000) for 1655 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 17: After refmac, R = 0.1851 (Rfree = 0.000) for 1647 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.1640 (Rfree = 0.000) for 1639 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.1540 (Rfree = 0.000) for 1633 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.1588 (Rfree = 0.000) for 1627 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.41 Search for helices and strands: 0 residues in 0 chains, 1688 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.321 Round 2: 111 peptides, 18 chains. Longest chain 12 peptides. Score 0.452 Round 3: 122 peptides, 19 chains. Longest chain 15 peptides. Score 0.493 Round 4: 113 peptides, 16 chains. Longest chain 17 peptides. Score 0.518 Round 5: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.424 Taking the results from Round 4 Chains 17, Residues 97, Estimated correctness of the model 17.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3721 restraints for refining 1679 atoms. 3323 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2105 (Rfree = 0.000) for 1679 atoms. Found 12 (15 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.2416 (Rfree = 0.000) for 1668 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 23: After refmac, R = 0.2518 (Rfree = 0.000) for 1663 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.1972 (Rfree = 0.000) for 1658 atoms. Found 9 (14 requested) and removed 21 (7 requested) atoms. Cycle 25: After refmac, R = 0.1878 (Rfree = 0.000) for 1641 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.47 Search for helices and strands: 0 residues in 0 chains, 1709 seeds are put forward Round 1: 82 peptides, 14 chains. Longest chain 13 peptides. Score 0.374 Round 2: 95 peptides, 13 chains. Longest chain 16 peptides. Score 0.490 Round 3: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.420 Round 4: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.443 Round 5: 82 peptides, 11 chains. Longest chain 15 peptides. Score 0.465 Taking the results from Round 2 Chains 13, Residues 82, Estimated correctness of the model 8.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3693 restraints for refining 1641 atoms. 3378 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2118 (Rfree = 0.000) for 1641 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 27: After refmac, R = 0.1932 (Rfree = 0.000) for 1637 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2313 (Rfree = 0.000) for 1632 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.1676 (Rfree = 0.000) for 1628 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.1626 (Rfree = 0.000) for 1623 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.46 Search for helices and strands: 0 residues in 0 chains, 1682 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.304 Round 2: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.388 Round 3: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.404 Round 4: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.440 Round 5: 106 peptides, 15 chains. Longest chain 18 peptides. Score 0.503 Taking the results from Round 5 Chains 16, Residues 91, Estimated correctness of the model 12.2 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3548 restraints for refining 1673 atoms. 3160 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1857 (Rfree = 0.000) for 1673 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.1705 (Rfree = 0.000) for 1665 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.1643 (Rfree = 0.000) for 1653 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1654 (Rfree = 0.000) for 1647 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1610 (Rfree = 0.000) for 1639 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 3.41 Search for helices and strands: 0 residues in 0 chains, 1700 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 11 peptides. Score 0.326 Round 2: 90 peptides, 14 chains. Longest chain 14 peptides. Score 0.429 Round 3: 99 peptides, 15 chains. Longest chain 18 peptides. Score 0.459 Round 4: 100 peptides, 13 chains. Longest chain 17 peptides. Score 0.520 Round 5: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 4 Chains 13, Residues 87, Estimated correctness of the model 17.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3737 restraints for refining 1666 atoms. 3402 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2271 (Rfree = 0.000) for 1666 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.2067 (Rfree = 0.000) for 1662 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.1900 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1599 (Rfree = 0.000) for 1668 atoms. Found 9 (14 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1456 (Rfree = 0.000) for 1670 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 1715 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 10 peptides. Score 0.323 Round 2: 108 peptides, 17 chains. Longest chain 15 peptides. Score 0.461 Round 3: 113 peptides, 16 chains. Longest chain 14 peptides. Score 0.518 Round 4: 104 peptides, 16 chains. Longest chain 15 peptides. Score 0.463 Round 5: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.405 Taking the results from Round 3 Chains 16, Residues 97, Estimated correctness of the model 17.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3746 reflections ( 99.76 % complete ) and 3806 restraints for refining 1692 atoms. 3434 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1734 (Rfree = 0.000) for 1692 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.1670 (Rfree = 0.000) for 1689 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1754 (Rfree = 0.000) for 1689 atoms. Found 14 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1508 (Rfree = 0.000) for 1696 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1509 (Rfree = 0.000) for 1689 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 1732 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.325 Round 2: 88 peptides, 13 chains. Longest chain 15 peptides. Score 0.446 Round 3: 89 peptides, 14 chains. Longest chain 11 peptides. Score 0.423 Round 4: 100 peptides, 13 chains. Longest chain 16 peptides. Score 0.520 Round 5: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.427 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 87, Estimated correctness of the model 17.6 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2etj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3746 reflections ( 99.76 % complete ) and 3811 restraints for refining 1703 atoms. 3462 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1718 (Rfree = 0.000) for 1703 atoms. Found 0 (15 requested) and removed 3 (7 requested) atoms. Cycle 47: After refmac, R = 0.1704 (Rfree = 0.000) for 1699 atoms. Found 0 (15 requested) and removed 1 (7 requested) atoms. Cycle 48: After refmac, R = 0.1842 (Rfree = 0.000) for 1698 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1528 (Rfree = 0.000) for 1688 atoms. TimeTaking 31.17