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 1zko-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.4-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/1zko-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.4-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/1zko-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.4-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 173 and 0 Target number of residues in the AU: 173 Target solvent content: 0.6164 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-3.4-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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2176 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 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: 47.500 3.400 Wilson plot Bfac: 59.44 3355 reflections ( 92.37 % complete ) and 0 restraints for refining 2425 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3505 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3496 (Rfree = 0.000) for 2425 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 2442 seeds are put forward NCS extension: 0 residues added, 2442 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 8 peptides. Score 0.226 Round 2: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.213 Round 3: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.249 Round 4: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.317 Round 5: 70 peptides, 12 chains. Longest chain 13 peptides. Score 0.347 Taking the results from Round 5 Chains 12, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4786 restraints for refining 1979 atoms. 4566 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2809 (Rfree = 0.000) for 1979 atoms. Found 3 (14 requested) and removed 16 (7 requested) atoms. Cycle 2: After refmac, R = 0.3200 (Rfree = 0.000) for 1955 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.3055 (Rfree = 0.000) for 1952 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2951 (Rfree = 0.000) for 1950 atoms. Found 12 (14 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.2878 (Rfree = 0.000) for 1942 atoms. Found 13 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 1964 seeds are put forward NCS extension: 0 residues added, 1964 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.209 Round 2: 98 peptides, 21 chains. Longest chain 7 peptides. Score 0.272 Round 3: 109 peptides, 23 chains. Longest chain 10 peptides. Score 0.292 Round 4: 106 peptides, 22 chains. Longest chain 8 peptides. Score 0.300 Round 5: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.329 Taking the results from Round 5 Chains 21, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4042 restraints for refining 1778 atoms. 3723 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2829 (Rfree = 0.000) for 1778 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 7: After refmac, R = 0.2832 (Rfree = 0.000) for 1773 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.2807 (Rfree = 0.000) for 1764 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.2674 (Rfree = 0.000) for 1760 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2589 (Rfree = 0.000) for 1753 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.69 Search for helices and strands: 0 residues in 0 chains, 1786 seeds are put forward NCS extension: 0 residues added, 1786 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 9 peptides. Score 0.250 Round 2: 98 peptides, 20 chains. Longest chain 12 peptides. Score 0.302 Round 3: 107 peptides, 21 chains. Longest chain 11 peptides. Score 0.336 Round 4: 104 peptides, 20 chains. Longest chain 15 peptides. Score 0.344 Round 5: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.322 Taking the results from Round 4 Chains 20, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4123 restraints for refining 1794 atoms. 3807 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2874 (Rfree = 0.000) for 1794 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 12: After refmac, R = 0.2943 (Rfree = 0.000) for 1778 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.2812 (Rfree = 0.000) for 1775 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2717 (Rfree = 0.000) for 1774 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2426 (Rfree = 0.000) for 1778 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 0 residues added, 1834 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 9 peptides. Score 0.240 Round 2: 98 peptides, 21 chains. Longest chain 9 peptides. Score 0.272 Round 3: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.286 Round 4: 118 peptides, 24 chains. Longest chain 9 peptides. Score 0.325 Round 5: 119 peptides, 24 chains. Longest chain 9 peptides. Score 0.332 Taking the results from Round 5 Chains 24, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 3783 restraints for refining 1726 atoms. 3427 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2917 (Rfree = 0.000) for 1726 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.2865 (Rfree = 0.000) for 1715 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2799 (Rfree = 0.000) for 1714 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2682 (Rfree = 0.000) for 1713 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2703 (Rfree = 0.000) for 1707 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 1746 seeds are put forward NCS extension: 0 residues added, 1746 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.241 Round 2: 96 peptides, 18 chains. Longest chain 15 peptides. Score 0.347 Round 3: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.370 Round 4: 112 peptides, 22 chains. Longest chain 9 peptides. Score 0.341 Round 5: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.433 Taking the results from Round 5 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4035 restraints for refining 1817 atoms. 3689 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2792 (Rfree = 0.000) for 1817 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.2666 (Rfree = 0.000) for 1817 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.2711 (Rfree = 0.000) for 1812 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2679 (Rfree = 0.000) for 1806 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2715 (Rfree = 0.000) for 1804 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.85 Search for helices and strands: 0 residues in 0 chains, 1836 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1845 seeds are put forward Round 1: 84 peptides, 19 chains. Longest chain 7 peptides. Score 0.229 Round 2: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.333 Round 3: 99 peptides, 18 chains. Longest chain 13 peptides. Score 0.368 Round 4: 100 peptides, 19 chains. Longest chain 8 peptides. Score 0.346 Round 5: 104 peptides, 17 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 5 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4241 restraints for refining 1888 atoms. 3910 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2755 (Rfree = 0.000) for 1888 atoms. Found 8 (14 requested) and removed 36 (7 requested) atoms. Cycle 27: After refmac, R = 0.2517 (Rfree = 0.000) for 1848 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2327 (Rfree = 0.000) for 1843 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2394 (Rfree = 0.000) for 1835 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.2422 (Rfree = 0.000) for 1830 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.58 Search for helices and strands: 0 residues in 0 chains, 1865 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1876 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.231 Round 2: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.282 Round 3: 70 peptides, 15 chains. Longest chain 6 peptides. Score 0.249 Round 4: 74 peptides, 15 chains. Longest chain 10 peptides. Score 0.280 Round 5: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 5 Chains 14, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4048 restraints for refining 1812 atoms. 3802 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2395 (Rfree = 0.000) for 1812 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.2345 (Rfree = 0.000) for 1805 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2240 (Rfree = 0.000) for 1798 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2205 (Rfree = 0.000) for 1793 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.2734 (Rfree = 0.000) for 1786 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.61 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 0 residues added, 1821 seeds are put forward Round 1: 63 peptides, 15 chains. Longest chain 6 peptides. Score 0.192 Round 2: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.257 Round 3: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.289 Round 4: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.288 Round 5: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.302 Taking the results from Round 5 Chains 12, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4036 restraints for refining 1765 atoms. 3840 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2367 (Rfree = 0.000) for 1765 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 37: After refmac, R = 0.2358 (Rfree = 0.000) for 1763 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2241 (Rfree = 0.000) for 1763 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2098 (Rfree = 0.000) for 1758 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2073 (Rfree = 0.000) for 1756 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 3.56 Search for helices and strands: 0 residues in 0 chains, 1779 seeds are put forward NCS extension: 0 residues added, 1779 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 11 peptides. Score 0.302 Round 2: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.286 Round 3: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.309 Round 4: 72 peptides, 11 chains. Longest chain 13 peptides. Score 0.393 Round 5: 76 peptides, 13 chains. Longest chain 13 peptides. Score 0.358 Taking the results from Round 4 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 3717 restraints for refining 1708 atoms. 3484 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2629 (Rfree = 0.000) for 1708 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.2344 (Rfree = 0.000) for 1703 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2408 (Rfree = 0.000) for 1700 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.2228 (Rfree = 0.000) for 1699 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.2208 (Rfree = 0.000) for 1699 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.55 Search for helices and strands: 0 residues in 0 chains, 1720 seeds are put forward NCS extension: 0 residues added, 1720 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 5 peptides. Score 0.205 Round 2: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.289 Round 3: 54 peptides, 10 chains. Longest chain 7 peptides. Score 0.292 Round 4: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.284 Round 5: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.267 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3355 reflections ( 92.37 % complete ) and 3691 restraints for refining 1663 atoms. 3525 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2347 (Rfree = 0.000) for 1663 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2398 (Rfree = 0.000) for 1652 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2055 (Rfree = 0.000) for 1642 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2028 (Rfree = 0.000) for 1633 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 29.88