null Sun 23 Dec 22:22:55 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 2i9w-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-1.8-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/2i9w-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-1.8-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 22:23:04 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/2i9w-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-1.8-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 184 and 0 Target number of residues in the AU: 184 Target solvent content: 0.4753 Checking the provided sequence file Detected sequence length: 184 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 184 Adjusted target solvent content: 0.48 Input MTZ file: 2i9w-1.8-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: 41.450 54.640 83.800 90.000 90.000 90.000 Input sequence file: 2i9w-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1472 target number of atoms Had to go as low as 0.45 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 1 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: 45.770 1.750 Wilson plot Bfac: 18.40 19799 reflections ( 99.78 % complete ) and 0 restraints for refining 1644 atoms. Observations/parameters ratio is 3.01 ------------------------------------------------------ Starting model: R = 0.3507 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3038 (Rfree = 0.000) for 1644 atoms. Found 61 (82 requested) and removed 46 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.90 1.95 Round 1: 122 peptides, 10 chains. Longest chain 27 peptides. Score 0.765 Round 2: 145 peptides, 8 chains. Longest chain 39 peptides. Score 0.867 Round 3: 155 peptides, 6 chains. Longest chain 45 peptides. Score 0.909 Round 4: 152 peptides, 6 chains. Longest chain 39 peptides. Score 0.904 Round 5: 155 peptides, 7 chains. Longest chain 39 peptides. Score 0.898 Taking the results from Round 3 Chains 8, Residues 149, Estimated correctness of the model 99.4 % 5 chains (138 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 80 A Built loop between residues 123 A and 129 A 6 chains (156 residues) following loop building 3 chains (145 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1714 restraints for refining 1557 atoms. 498 conditional restraints added. Observations/parameters ratio is 3.18 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3230 (Rfree = 0.000) for 1557 atoms. Found 46 (78 requested) and removed 42 (39 requested) atoms. Cycle 2: After refmac, R = 0.2854 (Rfree = 0.000) for 1558 atoms. Found 47 (76 requested) and removed 39 (39 requested) atoms. Cycle 3: After refmac, R = 0.2678 (Rfree = 0.000) for 1550 atoms. Found 38 (75 requested) and removed 26 (39 requested) atoms. Cycle 4: After refmac, R = 0.2548 (Rfree = 0.000) for 1549 atoms. Found 31 (73 requested) and removed 16 (39 requested) atoms. Cycle 5: After refmac, R = 0.2480 (Rfree = 0.000) for 1560 atoms. Found 32 (72 requested) and removed 7 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.82 1.87 Round 1: 159 peptides, 7 chains. Longest chain 47 peptides. Score 0.905 Round 2: 165 peptides, 4 chains. Longest chain 77 peptides. Score 0.939 Round 3: 163 peptides, 6 chains. Longest chain 51 peptides. Score 0.920 Round 4: 164 peptides, 5 chains. Longest chain 77 peptides. Score 0.930 Round 5: 163 peptides, 6 chains. Longest chain 51 peptides. Score 0.920 Taking the results from Round 2 Chains 4, Residues 161, Estimated correctness of the model 99.7 % 4 chains (161 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 49 A Built loop between residues 124 A and 129 A Built loop between residues 142 A and 149 A 1 chains (180 residues) following loop building 1 chains (180 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1603 restraints for refining 1648 atoms. 137 conditional restraints added. Observations/parameters ratio is 3.00 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2617 (Rfree = 0.000) for 1648 atoms. Found 46 (75 requested) and removed 42 (41 requested) atoms. Cycle 7: After refmac, R = 0.2431 (Rfree = 0.000) for 1648 atoms. Found 30 (74 requested) and removed 41 (41 requested) atoms. Cycle 8: After refmac, R = 0.2326 (Rfree = 0.000) for 1634 atoms. Found 34 (72 requested) and removed 13 (41 requested) atoms. Cycle 9: After refmac, R = 0.2224 (Rfree = 0.000) for 1653 atoms. Found 37 (72 requested) and removed 20 (41 requested) atoms. Cycle 10: After refmac, R = 0.2180 (Rfree = 0.000) for 1667 atoms. Found 28 (71 requested) and removed 10 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.80 1.85 Round 1: 166 peptides, 6 chains. Longest chain 49 peptides. Score 0.924 Round 2: 170 peptides, 4 chains. Longest chain 80 peptides. Score 0.944 Round 3: 170 peptides, 5 chains. Longest chain 65 peptides. Score 0.937 Round 4: 171 peptides, 4 chains. Longest chain 80 peptides. Score 0.945 Round 5: 170 peptides, 5 chains. Longest chain 64 peptides. Score 0.937 Taking the results from Round 4 Chains 4, Residues 167, Estimated correctness of the model 99.8 % 4 chains (167 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 125 A and 129 A Built loop between residues 142 A and 148 A 1 chains (182 residues) following loop building 1 chains (182 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1607 restraints for refining 1688 atoms. 125 conditional restraints added. Observations/parameters ratio is 2.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2452 (Rfree = 0.000) for 1688 atoms. Found 44 (72 requested) and removed 45 (42 requested) atoms. Cycle 12: After refmac, R = 0.2247 (Rfree = 0.000) for 1683 atoms. Found 40 (71 requested) and removed 31 (42 requested) atoms. Cycle 13: After refmac, R = 0.2172 (Rfree = 0.000) for 1691 atoms. Found 46 (69 requested) and removed 18 (42 requested) atoms. Cycle 14: After refmac, R = 0.2120 (Rfree = 0.000) for 1714 atoms. Found 35 (71 requested) and removed 17 (43 requested) atoms. Cycle 15: After refmac, R = 0.2081 (Rfree = 0.000) for 1730 atoms. Found 34 (71 requested) and removed 14 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.81 1.86 Round 1: 168 peptides, 6 chains. Longest chain 49 peptides. Score 0.927 Round 2: 170 peptides, 4 chains. Longest chain 80 peptides. Score 0.944 Round 3: 171 peptides, 4 chains. Longest chain 81 peptides. Score 0.945 Round 4: 169 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Round 5: 170 peptides, 4 chains. Longest chain 80 peptides. Score 0.944 Taking the results from Round 3 Chains 4, Residues 167, Estimated correctness of the model 99.8 % 4 chains (167 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 46 A Built loop between residues 125 A and 130 A Built loop between residues 142 A and 148 A 1 chains (182 residues) following loop building 1 chains (182 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1636 restraints for refining 1729 atoms. 154 conditional restraints added. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2395 (Rfree = 0.000) for 1729 atoms. Found 46 (71 requested) and removed 45 (43 requested) atoms. Cycle 17: After refmac, R = 0.2237 (Rfree = 0.000) for 1726 atoms. Found 43 (69 requested) and removed 27 (43 requested) atoms. Cycle 18: After refmac, R = 0.2150 (Rfree = 0.000) for 1740 atoms. Found 35 (68 requested) and removed 14 (43 requested) atoms. Cycle 19: After refmac, R = 0.2093 (Rfree = 0.000) for 1759 atoms. Found 32 (69 requested) and removed 13 (44 requested) atoms. Cycle 20: After refmac, R = 0.2027 (Rfree = 0.000) for 1777 atoms. Found 41 (69 requested) and removed 19 (44 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.81 1.86 Round 1: 170 peptides, 4 chains. Longest chain 79 peptides. Score 0.944 Round 2: 170 peptides, 4 chains. Longest chain 79 peptides. Score 0.944 Round 3: 170 peptides, 4 chains. Longest chain 79 peptides. Score 0.944 Round 4: 170 peptides, 5 chains. Longest chain 54 peptides. Score 0.937 Round 5: 169 peptides, 6 chains. Longest chain 57 peptides. Score 0.928 Taking the results from Round 3 Chains 4, Residues 166, Estimated correctness of the model 99.8 % 4 chains (166 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 124 A and 129 A Built loop between residues 142 A and 148 A 1 chains (182 residues) following loop building 1 chains (182 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1648 restraints for refining 1746 atoms. 166 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2372 (Rfree = 0.000) for 1746 atoms. Found 41 (68 requested) and removed 44 (43 requested) atoms. Cycle 22: After refmac, R = 0.2178 (Rfree = 0.000) for 1739 atoms. Found 36 (66 requested) and removed 28 (43 requested) atoms. Cycle 23: After refmac, R = 0.2116 (Rfree = 0.000) for 1746 atoms. Found 37 (64 requested) and removed 14 (43 requested) atoms. Cycle 24: After refmac, R = 0.2084 (Rfree = 0.000) for 1767 atoms. Found 26 (65 requested) and removed 11 (44 requested) atoms. Cycle 25: After refmac, R = 0.2033 (Rfree = 0.000) for 1781 atoms. Found 31 (66 requested) and removed 14 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.80 1.85 Round 1: 168 peptides, 5 chains. Longest chain 59 peptides. Score 0.935 Round 2: 167 peptides, 6 chains. Longest chain 54 peptides. Score 0.925 Round 3: 168 peptides, 5 chains. Longest chain 59 peptides. Score 0.935 Round 4: 169 peptides, 4 chains. Longest chain 80 peptides. Score 0.943 Round 5: 169 peptides, 4 chains. Longest chain 80 peptides. Score 0.943 Taking the results from Round 5 Chains 4, Residues 165, Estimated correctness of the model 99.8 % 4 chains (165 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 125 A and 129 A Built loop between residues 141 A and 148 A 1 chains (181 residues) following loop building 1 chains (181 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1665 restraints for refining 1743 atoms. 191 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2347 (Rfree = 0.000) for 1743 atoms. Found 51 (64 requested) and removed 44 (43 requested) atoms. Cycle 27: After refmac, R = 0.2189 (Rfree = 0.000) for 1746 atoms. Found 43 (63 requested) and removed 27 (43 requested) atoms. Cycle 28: After refmac, R = 0.2116 (Rfree = 0.000) for 1761 atoms. Found 41 (62 requested) and removed 21 (44 requested) atoms. Cycle 29: After refmac, R = 0.2087 (Rfree = 0.000) for 1779 atoms. Found 39 (61 requested) and removed 19 (44 requested) atoms. Cycle 30: After refmac, R = 0.2038 (Rfree = 0.000) for 1798 atoms. Found 39 (61 requested) and removed 32 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.79 1.84 Round 1: 165 peptides, 6 chains. Longest chain 43 peptides. Score 0.923 Round 2: 167 peptides, 5 chains. Longest chain 54 peptides. Score 0.934 Round 3: 168 peptides, 5 chains. Longest chain 57 peptides. Score 0.935 Round 4: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Round 5: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Taking the results from Round 5 Chains 4, Residues 164, Estimated correctness of the model 99.8 % 4 chains (164 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 124 A and 129 A Built loop between residues 141 A and 148 A 1 chains (181 residues) following loop building 1 chains (181 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1651 restraints for refining 1744 atoms. 177 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2341 (Rfree = 0.000) for 1744 atoms. Found 55 (57 requested) and removed 45 (43 requested) atoms. Cycle 32: After refmac, R = 0.2201 (Rfree = 0.000) for 1750 atoms. Found 46 (56 requested) and removed 31 (43 requested) atoms. Cycle 33: After refmac, R = 0.2133 (Rfree = 0.000) for 1763 atoms. Found 32 (55 requested) and removed 19 (44 requested) atoms. Cycle 34: After refmac, R = 0.2100 (Rfree = 0.000) for 1776 atoms. Found 37 (53 requested) and removed 18 (44 requested) atoms. Cycle 35: After refmac, R = 0.2053 (Rfree = 0.000) for 1793 atoms. Found 42 (53 requested) and removed 28 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.82 1.87 Round 1: 166 peptides, 5 chains. Longest chain 63 peptides. Score 0.932 Round 2: 166 peptides, 5 chains. Longest chain 58 peptides. Score 0.932 Round 3: 164 peptides, 6 chains. Longest chain 51 peptides. Score 0.922 Round 4: 165 peptides, 5 chains. Longest chain 59 peptides. Score 0.931 Round 5: 166 peptides, 4 chains. Longest chain 77 peptides. Score 0.940 Taking the results from Round 5 Chains 4, Residues 162, Estimated correctness of the model 99.7 % 4 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 49 A Built loop between residues 124 A and 129 A Built loop between residues 141 A and 148 A 1 chains (181 residues) following loop building 1 chains (181 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1655 restraints for refining 1741 atoms. 181 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2370 (Rfree = 0.000) for 1741 atoms. Found 47 (50 requested) and removed 43 (43 requested) atoms. Cycle 37: After refmac, R = 0.2181 (Rfree = 0.000) for 1744 atoms. Found 41 (49 requested) and removed 36 (43 requested) atoms. Cycle 38: After refmac, R = 0.2103 (Rfree = 0.000) for 1748 atoms. Found 32 (47 requested) and removed 18 (43 requested) atoms. Cycle 39: After refmac, R = 0.2078 (Rfree = 0.000) for 1761 atoms. Found 31 (46 requested) and removed 14 (44 requested) atoms. Cycle 40: After refmac, R = 0.2054 (Rfree = 0.000) for 1777 atoms. Found 35 (46 requested) and removed 20 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.80 1.85 Round 1: 167 peptides, 5 chains. Longest chain 64 peptides. Score 0.934 Round 2: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Round 3: 167 peptides, 5 chains. Longest chain 58 peptides. Score 0.934 Round 4: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Round 5: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Taking the results from Round 5 Chains 4, Residues 164, Estimated correctness of the model 99.8 % 4 chains (164 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 124 A and 129 A Built loop between residues 141 A and 148 A 1 chains (181 residues) following loop building 1 chains (181 residues) in sequence following loop building ------------------------------------------------------ 19799 reflections ( 99.78 % complete ) and 1680 restraints for refining 1748 atoms. 206 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2301 (Rfree = 0.000) for 1748 atoms. Found 43 (43 requested) and removed 46 (43 requested) atoms. Cycle 42: After refmac, R = 0.2156 (Rfree = 0.000) for 1742 atoms. Found 43 (43 requested) and removed 21 (43 requested) atoms. Cycle 43: After refmac, R = 0.2099 (Rfree = 0.000) for 1762 atoms. Found 34 (44 requested) and removed 14 (44 requested) atoms. Cycle 44: After refmac, R = 0.2062 (Rfree = 0.000) for 1781 atoms. Found 31 (44 requested) and removed 17 (44 requested) atoms. Cycle 45: After refmac, R = 0.2019 (Rfree = 0.000) for 1795 atoms. Found 30 (44 requested) and removed 20 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.81 1.86 Round 1: 168 peptides, 5 chains. Longest chain 65 peptides. Score 0.935 Round 2: 167 peptides, 5 chains. Longest chain 58 peptides. Score 0.934 Round 3: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Round 4: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Round 5: 168 peptides, 4 chains. Longest chain 79 peptides. Score 0.943 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 164, Estimated correctness of the model 99.8 % 4 chains (164 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 124 A and 129 A Built loop between residues 141 A and 148 A 1 chains (181 residues) following loop building 1 chains (181 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19799 reflections ( 99.78 % complete ) and 1474 restraints for refining 1439 atoms. Observations/parameters ratio is 3.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2948 (Rfree = 0.000) for 1439 atoms. Found 19 (36 requested) and removed 0 (36 requested) atoms. Cycle 47: After refmac, R = 0.2761 (Rfree = 0.000) for 1439 atoms. Found 6 (36 requested) and removed 0 (36 requested) atoms. Cycle 48: After refmac, R = 0.2645 (Rfree = 0.000) for 1439 atoms. Found 4 (36 requested) and removed 0 (36 requested) atoms. Cycle 49: After refmac, R = 0.2581 (Rfree = 0.000) for 1439 atoms. Found 1 (36 requested) and removed 0 (36 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:07:02 GMT 2018 Job finished. TimeTaking 44.11 Used memory is bytes: 9492936