null Tue 25 Dec 19:27:55 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 2ghs-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-1.6-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/2ghs-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-1.6-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 ============================================================ Tue 25 Dec 19:28:05 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/2ghs-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-1.6-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 303 and 0 Target number of residues in the AU: 303 Target solvent content: 0.4257 Checking the provided sequence file Detected sequence length: 326 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 326 Adjusted target solvent content: 0.38 Input MTZ file: 2ghs-1.6-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: 46.258 75.703 81.538 90.000 90.000 90.000 Input sequence file: 2ghs-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.30 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: 55.478 1.551 Wilson plot Bfac: 11.07 32435 reflections ( 76.79 % complete ) and 0 restraints for refining 2877 atoms. Observations/parameters ratio is 2.82 ------------------------------------------------------ Starting model: R = 0.3287 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2753 (Rfree = 0.000) for 2877 atoms. Found 143 (203 requested) and removed 110 (101 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.60 1.88 Round 1: 263 peptides, 11 chains. Longest chain 107 peptides. Score 0.924 Round 2: 278 peptides, 7 chains. Longest chain 103 peptides. Score 0.953 Round 3: 285 peptides, 3 chains. Longest chain 194 peptides. Score 0.971 Round 4: 285 peptides, 3 chains. Longest chain 194 peptides. Score 0.971 Round 5: 285 peptides, 4 chains. Longest chain 120 peptides. Score 0.968 Taking the results from Round 4 Chains 4, Residues 282, Estimated correctness of the model 100.0 % 3 chains (277 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 226 A and 230 A 3 chains (285 residues) following loop building 2 chains (280 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2662 restraints for refining 2640 atoms. 461 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2786 (Rfree = 0.000) for 2640 atoms. Found 82 (186 requested) and removed 87 (93 requested) atoms. Cycle 2: After refmac, R = 0.2487 (Rfree = 0.000) for 2625 atoms. Found 78 (182 requested) and removed 18 (93 requested) atoms. Cycle 3: After refmac, R = 0.2227 (Rfree = 0.000) for 2678 atoms. Found 68 (185 requested) and removed 21 (94 requested) atoms. Cycle 4: After refmac, R = 0.2114 (Rfree = 0.000) for 2719 atoms. Found 64 (188 requested) and removed 20 (96 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 2750 atoms. Found 63 (191 requested) and removed 30 (97 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.49 1.75 Round 1: 284 peptides, 5 chains. Longest chain 156 peptides. Score 0.964 Round 2: 288 peptides, 4 chains. Longest chain 160 peptides. Score 0.969 Round 3: 285 peptides, 4 chains. Longest chain 160 peptides. Score 0.968 Round 4: 286 peptides, 3 chains. Longest chain 208 peptides. Score 0.972 Round 5: 286 peptides, 3 chains. Longest chain 210 peptides. Score 0.972 Taking the results from Round 5 Chains 3, Residues 283, Estimated correctness of the model 100.0 % 3 chains (283 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 292 A and 300 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2595 restraints for refining 2693 atoms. 319 conditional restraints added. Observations/parameters ratio is 3.01 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2355 (Rfree = 0.000) for 2693 atoms. Found 82 (186 requested) and removed 53 (95 requested) atoms. Cycle 7: After refmac, R = 0.2094 (Rfree = 0.000) for 2718 atoms. Found 68 (184 requested) and removed 13 (96 requested) atoms. Cycle 8: After refmac, R = 0.2006 (Rfree = 0.000) for 2766 atoms. Found 63 (188 requested) and removed 28 (98 requested) atoms. Cycle 9: After refmac, R = 0.1933 (Rfree = 0.000) for 2797 atoms. Found 61 (190 requested) and removed 20 (99 requested) atoms. Cycle 10: After refmac, R = 0.1894 (Rfree = 0.000) for 2831 atoms. Found 64 (192 requested) and removed 32 (100 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.48 1.74 Round 1: 287 peptides, 3 chains. Longest chain 208 peptides. Score 0.972 Round 2: 287 peptides, 4 chains. Longest chain 201 peptides. Score 0.968 Round 3: 287 peptides, 4 chains. Longest chain 198 peptides. Score 0.968 Round 4: 287 peptides, 4 chains. Longest chain 200 peptides. Score 0.968 Round 5: 288 peptides, 3 chains. Longest chain 212 peptides. Score 0.972 Taking the results from Round 5 Chains 3, Residues 285, Estimated correctness of the model 100.0 % 3 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 82 A Built loop between residues 292 A and 298 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2598 restraints for refining 2716 atoms. 322 conditional restraints added. Observations/parameters ratio is 2.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2172 (Rfree = 0.000) for 2716 atoms. Found 107 (184 requested) and removed 41 (96 requested) atoms. Cycle 12: After refmac, R = 0.1993 (Rfree = 0.000) for 2779 atoms. Found 72 (188 requested) and removed 19 (98 requested) atoms. Cycle 13: After refmac, R = 0.1943 (Rfree = 0.000) for 2824 atoms. Found 56 (192 requested) and removed 32 (100 requested) atoms. Cycle 14: After refmac, R = 0.1893 (Rfree = 0.000) for 2844 atoms. Found 65 (189 requested) and removed 32 (100 requested) atoms. Cycle 15: After refmac, R = 0.1856 (Rfree = 0.000) for 2874 atoms. Found 68 (191 requested) and removed 35 (101 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.48 1.74 Round 1: 290 peptides, 4 chains. Longest chain 198 peptides. Score 0.969 Round 2: 290 peptides, 3 chains. Longest chain 211 peptides. Score 0.973 Round 3: 289 peptides, 4 chains. Longest chain 202 peptides. Score 0.969 Round 4: 289 peptides, 4 chains. Longest chain 198 peptides. Score 0.969 Round 5: 290 peptides, 3 chains. Longest chain 211 peptides. Score 0.973 Taking the results from Round 5 Chains 4, Residues 287, Estimated correctness of the model 100.0 % 3 chains (286 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 292 A and 297 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2619 restraints for refining 2736 atoms. 343 conditional restraints added. Observations/parameters ratio is 2.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2159 (Rfree = 0.000) for 2736 atoms. Found 97 (178 requested) and removed 40 (96 requested) atoms. Cycle 17: After refmac, R = 0.1977 (Rfree = 0.000) for 2789 atoms. Found 78 (181 requested) and removed 19 (98 requested) atoms. Cycle 18: After refmac, R = 0.1940 (Rfree = 0.000) for 2842 atoms. Found 59 (185 requested) and removed 27 (100 requested) atoms. Cycle 19: After refmac, R = 0.1874 (Rfree = 0.000) for 2868 atoms. Found 65 (187 requested) and removed 29 (101 requested) atoms. Cycle 20: After refmac, R = 0.1857 (Rfree = 0.000) for 2896 atoms. Found 73 (189 requested) and removed 38 (102 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.49 1.75 Round 1: 288 peptides, 3 chains. Longest chain 209 peptides. Score 0.972 Round 2: 288 peptides, 3 chains. Longest chain 211 peptides. Score 0.972 Round 3: 288 peptides, 3 chains. Longest chain 213 peptides. Score 0.972 Round 4: 288 peptides, 3 chains. Longest chain 209 peptides. Score 0.972 Round 5: 288 peptides, 3 chains. Longest chain 211 peptides. Score 0.972 Taking the results from Round 5 Chains 3, Residues 285, Estimated correctness of the model 100.0 % 3 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 293 A and 299 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2598 restraints for refining 2746 atoms. 322 conditional restraints added. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2159 (Rfree = 0.000) for 2746 atoms. Found 110 (175 requested) and removed 32 (97 requested) atoms. Cycle 22: After refmac, R = 0.1961 (Rfree = 0.000) for 2822 atoms. Found 69 (179 requested) and removed 23 (99 requested) atoms. Cycle 23: After refmac, R = 0.1922 (Rfree = 0.000) for 2855 atoms. Found 64 (182 requested) and removed 23 (101 requested) atoms. Cycle 24: After refmac, R = 0.1887 (Rfree = 0.000) for 2893 atoms. Found 61 (184 requested) and removed 25 (102 requested) atoms. Cycle 25: After refmac, R = 0.1846 (Rfree = 0.000) for 2921 atoms. Found 57 (186 requested) and removed 32 (103 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.48 1.74 Round 1: 287 peptides, 4 chains. Longest chain 158 peptides. Score 0.968 Round 2: 287 peptides, 4 chains. Longest chain 200 peptides. Score 0.968 Round 3: 288 peptides, 3 chains. Longest chain 250 peptides. Score 0.972 Round 4: 288 peptides, 3 chains. Longest chain 210 peptides. Score 0.972 Round 5: 288 peptides, 3 chains. Longest chain 212 peptides. Score 0.972 Taking the results from Round 5 Chains 3, Residues 285, Estimated correctness of the model 100.0 % 3 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 294 A and 300 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2609 restraints for refining 2800 atoms. 333 conditional restraints added. Observations/parameters ratio is 2.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2142 (Rfree = 0.000) for 2800 atoms. Found 113 (173 requested) and removed 44 (98 requested) atoms. Cycle 27: After refmac, R = 0.1974 (Rfree = 0.000) for 2864 atoms. Found 71 (178 requested) and removed 29 (101 requested) atoms. Cycle 28: After refmac, R = 0.1921 (Rfree = 0.000) for 2892 atoms. Found 67 (180 requested) and removed 30 (102 requested) atoms. Cycle 29: After refmac, R = 0.1867 (Rfree = 0.000) for 2925 atoms. Found 56 (182 requested) and removed 29 (103 requested) atoms. Cycle 30: After refmac, R = 0.1850 (Rfree = 0.000) for 2940 atoms. Found 71 (179 requested) and removed 32 (104 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.48 1.74 Round 1: 289 peptides, 3 chains. Longest chain 210 peptides. Score 0.973 Round 2: 287 peptides, 5 chains. Longest chain 144 peptides. Score 0.965 Round 3: 289 peptides, 3 chains. Longest chain 214 peptides. Score 0.973 Round 4: 289 peptides, 3 chains. Longest chain 210 peptides. Score 0.973 Round 5: 289 peptides, 3 chains. Longest chain 212 peptides. Score 0.973 Taking the results from Round 5 Chains 3, Residues 286, Estimated correctness of the model 100.0 % 3 chains (286 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 294 A and 299 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2609 restraints for refining 2796 atoms. 333 conditional restraints added. Observations/parameters ratio is 2.90 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2136 (Rfree = 0.000) for 2796 atoms. Found 114 (169 requested) and removed 39 (98 requested) atoms. Cycle 32: After refmac, R = 0.1968 (Rfree = 0.000) for 2870 atoms. Found 65 (174 requested) and removed 34 (101 requested) atoms. Cycle 33: After refmac, R = 0.1903 (Rfree = 0.000) for 2893 atoms. Found 65 (172 requested) and removed 34 (102 requested) atoms. Cycle 34: After refmac, R = 0.1874 (Rfree = 0.000) for 2919 atoms. Found 55 (169 requested) and removed 35 (103 requested) atoms. Cycle 35: After refmac, R = 0.1810 (Rfree = 0.000) for 2932 atoms. Found 79 (166 requested) and removed 38 (103 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.47 1.73 Round 1: 287 peptides, 4 chains. Longest chain 142 peptides. Score 0.968 Round 2: 286 peptides, 5 chains. Longest chain 144 peptides. Score 0.964 Round 3: 288 peptides, 3 chains. Longest chain 213 peptides. Score 0.972 Round 4: 286 peptides, 5 chains. Longest chain 142 peptides. Score 0.964 Round 5: 287 peptides, 4 chains. Longest chain 144 peptides. Score 0.968 Taking the results from Round 3 Chains 3, Residues 285, Estimated correctness of the model 100.0 % 3 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 82 A Built loop between residues 293 A and 299 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2608 restraints for refining 2785 atoms. 332 conditional restraints added. Observations/parameters ratio is 2.91 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2112 (Rfree = 0.000) for 2785 atoms. Found 112 (157 requested) and removed 32 (98 requested) atoms. Cycle 37: After refmac, R = 0.1974 (Rfree = 0.000) for 2858 atoms. Found 61 (162 requested) and removed 18 (101 requested) atoms. Cycle 38: After refmac, R = 0.1896 (Rfree = 0.000) for 2893 atoms. Found 58 (164 requested) and removed 29 (102 requested) atoms. Cycle 39: After refmac, R = 0.1838 (Rfree = 0.000) for 2918 atoms. Found 67 (165 requested) and removed 30 (103 requested) atoms. Cycle 40: After refmac, R = 0.1837 (Rfree = 0.000) for 2949 atoms. Found 60 (166 requested) and removed 49 (104 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.48 1.74 Round 1: 287 peptides, 3 chains. Longest chain 208 peptides. Score 0.972 Round 2: 286 peptides, 4 chains. Longest chain 200 peptides. Score 0.968 Round 3: 287 peptides, 3 chains. Longest chain 250 peptides. Score 0.972 Round 4: 287 peptides, 3 chains. Longest chain 208 peptides. Score 0.972 Round 5: 287 peptides, 3 chains. Longest chain 210 peptides. Score 0.972 Taking the results from Round 5 Chains 3, Residues 284, Estimated correctness of the model 100.0 % 3 chains (284 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 292 A and 299 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ 32435 reflections ( 76.79 % complete ) and 2645 restraints for refining 2811 atoms. 369 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2142 (Rfree = 0.000) for 2811 atoms. Found 121 (154 requested) and removed 44 (99 requested) atoms. Cycle 42: After refmac, R = 0.1972 (Rfree = 0.000) for 2884 atoms. Found 69 (159 requested) and removed 27 (102 requested) atoms. Cycle 43: After refmac, R = 0.1889 (Rfree = 0.000) for 2919 atoms. Found 58 (161 requested) and removed 26 (103 requested) atoms. Cycle 44: After refmac, R = 0.1863 (Rfree = 0.000) for 2943 atoms. Found 58 (162 requested) and removed 38 (104 requested) atoms. Cycle 45: After refmac, R = 0.1841 (Rfree = 0.000) for 2957 atoms. Found 67 (159 requested) and removed 33 (104 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.48 1.74 Round 1: 285 peptides, 5 chains. Longest chain 156 peptides. Score 0.964 Round 2: 286 peptides, 4 chains. Longest chain 200 peptides. Score 0.968 Round 3: 287 peptides, 3 chains. Longest chain 212 peptides. Score 0.972 Round 4: 288 peptides, 3 chains. Longest chain 208 peptides. Score 0.972 Round 5: 288 peptides, 3 chains. Longest chain 210 peptides. Score 0.972 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 285, Estimated correctness of the model 100.0 % 3 chains (285 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 292 A and 298 A 1 chains (292 residues) following loop building 1 chains (292 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 32435 reflections ( 76.79 % complete ) and 2276 restraints for refining 2223 atoms. Observations/parameters ratio is 3.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2790 (Rfree = 0.000) for 2223 atoms. Found 95 (119 requested) and removed 0 (119 requested) atoms. Cycle 47: After refmac, R = 0.2316 (Rfree = 0.000) for 2223 atoms. Found 41 (124 requested) and removed 0 (81 requested) atoms. Cycle 48: After refmac, R = 0.2147 (Rfree = 0.000) for 2223 atoms. Found 21 (126 requested) and removed 3 (83 requested) atoms. Cycle 49: After refmac, R = 0.2060 (Rfree = 0.000) for 2223 atoms. Found 15 (128 requested) and removed 2 (84 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:31:23 GMT 2018 Job finished. TimeTaking 63.46 Used memory is bytes: 10326528