null Sun 23 Dec 22:23:08 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 1vqz-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-2.0-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/1vqz-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-2.0-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 22:23:18 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/1vqz-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-2.0-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.4847 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.49 Input MTZ file: 1vqz-2.0-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: 19 Cell parameters: 45.503 70.280 113.629 90.000 90.000 90.000 Input sequence file: 1vqz-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 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: 59.771 1.990 Wilson plot Bfac: 20.41 25667 reflections ( 99.77 % complete ) and 0 restraints for refining 3025 atoms. Observations/parameters ratio is 2.12 ------------------------------------------------------ Starting model: R = 0.3317 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2871 (Rfree = 0.000) for 3025 atoms. Found 92 (105 requested) and removed 53 (52 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.00 2.03 Round 1: 230 peptides, 27 chains. Longest chain 16 peptides. Score 0.667 Round 2: 264 peptides, 16 chains. Longest chain 51 peptides. Score 0.845 Round 3: 276 peptides, 15 chains. Longest chain 50 peptides. Score 0.868 Round 4: 291 peptides, 9 chains. Longest chain 85 peptides. Score 0.917 Round 5: 284 peptides, 12 chains. Longest chain 51 peptides. Score 0.895 Taking the results from Round 4 Chains 9, Residues 282, Estimated correctness of the model 99.3 % 5 chains (256 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 52 A Built loop between residues 251 A and 255 A 7 chains (287 residues) following loop building 3 chains (261 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3109 restraints for refining 2853 atoms. 830 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3077 (Rfree = 0.000) for 2853 atoms. Found 91 (99 requested) and removed 54 (49 requested) atoms. Cycle 2: After refmac, R = 0.2772 (Rfree = 0.000) for 2883 atoms. Found 70 (98 requested) and removed 42 (50 requested) atoms. Cycle 3: After refmac, R = 0.2583 (Rfree = 0.000) for 2897 atoms. Found 57 (97 requested) and removed 16 (50 requested) atoms. Cycle 4: After refmac, R = 0.2468 (Rfree = 0.000) for 2932 atoms. Found 54 (98 requested) and removed 18 (51 requested) atoms. Cycle 5: After refmac, R = 0.2401 (Rfree = 0.000) for 2963 atoms. Found 57 (99 requested) and removed 22 (51 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.94 1.97 Round 1: 296 peptides, 5 chains. Longest chain 148 peptides. Score 0.940 Round 2: 295 peptides, 7 chains. Longest chain 91 peptides. Score 0.930 Round 3: 297 peptides, 6 chains. Longest chain 96 peptides. Score 0.936 Round 4: 296 peptides, 9 chains. Longest chain 91 peptides. Score 0.921 Round 5: 299 peptides, 6 chains. Longest chain 91 peptides. Score 0.937 Taking the results from Round 1 Chains 5, Residues 291, Estimated correctness of the model 99.6 % 5 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 52 A Built loop between residues 101 A and 111 A 3 chains (302 residues) following loop building 3 chains (302 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3007 restraints for refining 2987 atoms. 497 conditional restraints added. Observations/parameters ratio is 2.15 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2430 (Rfree = 0.000) for 2987 atoms. Found 96 (99 requested) and removed 53 (51 requested) atoms. Cycle 7: After refmac, R = 0.2287 (Rfree = 0.000) for 3022 atoms. Found 64 (99 requested) and removed 37 (52 requested) atoms. Cycle 8: After refmac, R = 0.2189 (Rfree = 0.000) for 3046 atoms. Found 67 (97 requested) and removed 16 (52 requested) atoms. Cycle 9: After refmac, R = 0.2088 (Rfree = 0.000) for 3095 atoms. Found 54 (98 requested) and removed 31 (53 requested) atoms. Cycle 10: After refmac, R = 0.2024 (Rfree = 0.000) for 3111 atoms. Found 63 (97 requested) and removed 28 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.94 1.97 Round 1: 301 peptides, 6 chains. Longest chain 97 peptides. Score 0.938 Round 2: 298 peptides, 9 chains. Longest chain 92 peptides. Score 0.922 Round 3: 300 peptides, 8 chains. Longest chain 54 peptides. Score 0.929 Round 4: 298 peptides, 8 chains. Longest chain 68 peptides. Score 0.927 Round 5: 301 peptides, 7 chains. Longest chain 55 peptides. Score 0.934 Taking the results from Round 1 Chains 6, Residues 295, Estimated correctness of the model 99.6 % 5 chains (246 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 108 A 5 chains (299 residues) following loop building 4 chains (250 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3520 restraints for refining 3028 atoms. 1255 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2227 (Rfree = 0.000) for 3028 atoms. Found 93 (94 requested) and removed 54 (52 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 3067 atoms. Found 63 (93 requested) and removed 19 (53 requested) atoms. Cycle 13: After refmac, R = 0.2010 (Rfree = 0.000) for 3107 atoms. Found 57 (95 requested) and removed 21 (54 requested) atoms. Cycle 14: After refmac, R = 0.1936 (Rfree = 0.000) for 3142 atoms. Found 59 (96 requested) and removed 26 (54 requested) atoms. Cycle 15: After refmac, R = 0.1897 (Rfree = 0.000) for 3173 atoms. Found 55 (97 requested) and removed 30 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.94 1.97 Round 1: 301 peptides, 5 chains. Longest chain 95 peptides. Score 0.943 Round 2: 301 peptides, 5 chains. Longest chain 100 peptides. Score 0.943 Round 3: 301 peptides, 9 chains. Longest chain 71 peptides. Score 0.925 Round 4: 302 peptides, 7 chains. Longest chain 89 peptides. Score 0.934 Round 5: 304 peptides, 6 chains. Longest chain 116 peptides. Score 0.940 Taking the results from Round 2 Chains 5, Residues 296, Estimated correctness of the model 99.6 % 4 chains (283 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 239 A and 242 A 4 chains (298 residues) following loop building 3 chains (285 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3201 restraints for refining 3076 atoms. 765 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2087 (Rfree = 0.000) for 3076 atoms. Found 91 (91 requested) and removed 55 (53 requested) atoms. Cycle 17: After refmac, R = 0.1988 (Rfree = 0.000) for 3110 atoms. Found 58 (91 requested) and removed 28 (54 requested) atoms. Cycle 18: After refmac, R = 0.1896 (Rfree = 0.000) for 3139 atoms. Found 61 (92 requested) and removed 23 (54 requested) atoms. Cycle 19: After refmac, R = 0.1853 (Rfree = 0.000) for 3174 atoms. Found 56 (92 requested) and removed 36 (55 requested) atoms. Cycle 20: After refmac, R = 0.1829 (Rfree = 0.000) for 3192 atoms. Found 68 (90 requested) and removed 36 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.94 1.97 Round 1: 304 peptides, 5 chains. Longest chain 97 peptides. Score 0.944 Round 2: 300 peptides, 8 chains. Longest chain 73 peptides. Score 0.929 Round 3: 298 peptides, 8 chains. Longest chain 113 peptides. Score 0.927 Round 4: 302 peptides, 6 chains. Longest chain 60 peptides. Score 0.939 Round 5: 299 peptides, 8 chains. Longest chain 85 peptides. Score 0.928 Taking the results from Round 1 Chains 6, Residues 299, Estimated correctness of the model 99.6 % 5 chains (294 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 105 A and 108 A Built loop between residues 237 A and 244 A 3 chains (302 residues) following loop building 3 chains (302 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3034 restraints for refining 3091 atoms. 527 conditional restraints added. Observations/parameters ratio is 2.08 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1994 (Rfree = 0.000) for 3091 atoms. Found 86 (86 requested) and removed 49 (53 requested) atoms. Cycle 22: After refmac, R = 0.1910 (Rfree = 0.000) for 3127 atoms. Found 57 (84 requested) and removed 27 (54 requested) atoms. Cycle 23: After refmac, R = 0.1841 (Rfree = 0.000) for 3156 atoms. Found 65 (85 requested) and removed 21 (54 requested) atoms. Cycle 24: After refmac, R = 0.1815 (Rfree = 0.000) for 3199 atoms. Found 52 (87 requested) and removed 49 (55 requested) atoms. Cycle 25: After refmac, R = 0.1800 (Rfree = 0.000) for 3200 atoms. Found 74 (84 requested) and removed 36 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.96 Round 1: 302 peptides, 6 chains. Longest chain 97 peptides. Score 0.939 Round 2: 302 peptides, 6 chains. Longest chain 98 peptides. Score 0.939 Round 3: 298 peptides, 10 chains. Longest chain 54 peptides. Score 0.917 Round 4: 306 peptides, 5 chains. Longest chain 118 peptides. Score 0.945 Round 5: 304 peptides, 7 chains. Longest chain 99 peptides. Score 0.936 Taking the results from Round 4 Chains 5, Residues 301, Estimated correctness of the model 99.7 % 4 chains (293 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 289 A and 292 A 4 chains (303 residues) following loop building 3 chains (295 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3099 restraints for refining 3093 atoms. 620 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1984 (Rfree = 0.000) for 3093 atoms. Found 81 (81 requested) and removed 49 (53 requested) atoms. Cycle 27: After refmac, R = 0.1917 (Rfree = 0.000) for 3122 atoms. Found 80 (80 requested) and removed 24 (54 requested) atoms. Cycle 28: After refmac, R = 0.1851 (Rfree = 0.000) for 3177 atoms. Found 66 (81 requested) and removed 39 (55 requested) atoms. Cycle 29: After refmac, R = 0.1820 (Rfree = 0.000) for 3204 atoms. Found 61 (80 requested) and removed 55 (55 requested) atoms. Cycle 30: After refmac, R = 0.1805 (Rfree = 0.000) for 3207 atoms. Found 75 (78 requested) and removed 40 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.96 Round 1: 307 peptides, 5 chains. Longest chain 118 peptides. Score 0.946 Round 2: 305 peptides, 7 chains. Longest chain 78 peptides. Score 0.936 Round 3: 303 peptides, 8 chains. Longest chain 66 peptides. Score 0.931 Round 4: 306 peptides, 5 chains. Longest chain 147 peptides. Score 0.945 Round 5: 303 peptides, 8 chains. Longest chain 104 peptides. Score 0.931 Taking the results from Round 1 Chains 5, Residues 302, Estimated correctness of the model 99.7 % 3 chains (198 residues) have been docked in sequence Building loops using Loopy2018 5 chains (302 residues) following loop building 3 chains (198 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3984 restraints for refining 3079 atoms. 1923 conditional restraints added. Observations/parameters ratio is 2.08 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2039 (Rfree = 0.000) for 3079 atoms. Found 73 (73 requested) and removed 49 (53 requested) atoms. Cycle 32: After refmac, R = 0.1954 (Rfree = 0.000) for 3099 atoms. Found 55 (71 requested) and removed 19 (53 requested) atoms. Cycle 33: After refmac, R = 0.1879 (Rfree = 0.000) for 3135 atoms. Found 61 (71 requested) and removed 16 (54 requested) atoms. Cycle 34: After refmac, R = 0.1842 (Rfree = 0.000) for 3179 atoms. Found 50 (73 requested) and removed 33 (55 requested) atoms. Cycle 35: After refmac, R = 0.1808 (Rfree = 0.000) for 3193 atoms. Found 52 (71 requested) and removed 23 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.92 1.95 Round 1: 306 peptides, 6 chains. Longest chain 97 peptides. Score 0.941 Round 2: 303 peptides, 8 chains. Longest chain 60 peptides. Score 0.931 Round 3: 305 peptides, 7 chains. Longest chain 78 peptides. Score 0.936 Round 4: 305 peptides, 7 chains. Longest chain 66 peptides. Score 0.936 Round 5: 304 peptides, 7 chains. Longest chain 79 peptides. Score 0.936 Taking the results from Round 1 Chains 7, Residues 300, Estimated correctness of the model 99.6 % 5 chains (287 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 237 A and 244 A 4 chains (303 residues) following loop building 3 chains (295 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 3117 restraints for refining 3115 atoms. 638 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1936 (Rfree = 0.000) for 3115 atoms. Found 69 (69 requested) and removed 47 (54 requested) atoms. Cycle 37: After refmac, R = 0.1853 (Rfree = 0.000) for 3133 atoms. Found 68 (68 requested) and removed 24 (54 requested) atoms. Cycle 38: After refmac, R = 0.1780 (Rfree = 0.000) for 3176 atoms. Found 68 (68 requested) and removed 29 (55 requested) atoms. Cycle 39: After refmac, R = 0.1774 (Rfree = 0.000) for 3214 atoms. Found 62 (69 requested) and removed 53 (55 requested) atoms. Cycle 40: After refmac, R = 0.1749 (Rfree = 0.000) for 3222 atoms. Found 67 (67 requested) and removed 56 (56 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.92 1.95 Round 1: 305 peptides, 6 chains. Longest chain 96 peptides. Score 0.941 Round 2: 306 peptides, 6 chains. Longest chain 78 peptides. Score 0.941 Round 3: 305 peptides, 6 chains. Longest chain 116 peptides. Score 0.941 Round 4: 303 peptides, 8 chains. Longest chain 60 peptides. Score 0.931 Round 5: 305 peptides, 6 chains. Longest chain 60 peptides. Score 0.941 Taking the results from Round 5 Chains 6, Residues 299, Estimated correctness of the model 99.6 % 6 chains (299 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 246 A and 249 A Built loop between residues 287 A and 290 A 3 chains (305 residues) following loop building 3 chains (305 residues) in sequence following loop building ------------------------------------------------------ 25667 reflections ( 99.77 % complete ) and 2976 restraints for refining 3105 atoms. 446 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1918 (Rfree = 0.000) for 3105 atoms. Found 62 (62 requested) and removed 47 (53 requested) atoms. Cycle 42: After refmac, R = 0.1830 (Rfree = 0.000) for 3119 atoms. Found 60 (60 requested) and removed 21 (54 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 3158 atoms. Found 61 (61 requested) and removed 30 (54 requested) atoms. Cycle 44: After refmac, R = 0.1752 (Rfree = 0.000) for 3187 atoms. Found 62 (62 requested) and removed 49 (55 requested) atoms. Cycle 45: After refmac, R = 0.1735 (Rfree = 0.000) for 3200 atoms. Found 60 (60 requested) and removed 41 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.96 Round 1: 306 peptides, 5 chains. Longest chain 96 peptides. Score 0.945 Round 2: 304 peptides, 7 chains. Longest chain 73 peptides. Score 0.936 Round 3: 303 peptides, 8 chains. Longest chain 79 peptides. Score 0.931 Round 4: 305 peptides, 6 chains. Longest chain 99 peptides. Score 0.941 Round 5: 306 peptides, 5 chains. Longest chain 118 peptides. Score 0.945 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 301, Estimated correctness of the model 99.7 % 4 chains (293 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 129 A and 141 A Built loop between residues 250 A and 253 A 3 chains (314 residues) following loop building 2 chains (306 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 25667 reflections ( 99.77 % complete ) and 2567 restraints for refining 2522 atoms. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2696 (Rfree = 0.000) for 2522 atoms. Found 45 (45 requested) and removed 0 (45 requested) atoms. Cycle 47: After refmac, R = 0.2494 (Rfree = 0.000) for 2522 atoms. Found 30 (46 requested) and removed 0 (44 requested) atoms. Cycle 48: After refmac, R = 0.2374 (Rfree = 0.000) for 2522 atoms. Found 20 (47 requested) and removed 0 (45 requested) atoms. Cycle 49: After refmac, R = 0.2276 (Rfree = 0.000) for 2522 atoms. Found 15 (47 requested) and removed 1 (45 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:20:39 GMT 2018 Job finished. TimeTaking 57.51 Used memory is bytes: 14134744