null 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 1vli-2.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vli-2.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vli-2.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-2.4-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/1vli-2.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-2.4-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/1vli-2.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-2.4-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 447 and 0 Target number of residues in the AU: 447 Target solvent content: 0.5910 Checking the provided sequence file Detected sequence length: 385 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 385 Adjusted target solvent content: 0.65 Input MTZ file: 1vli-2.4-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: 154 Cell parameters: 70.614 70.614 205.438 90.000 90.000 120.000 Input sequence file: 1vli-2.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3080 target number of atoms Had to go as low as 1.05 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: 68.479 2.380 Wilson plot Bfac: 48.87 24667 reflections ( 99.85 % complete ) and 0 restraints for refining 3420 atoms. Observations/parameters ratio is 1.80 ------------------------------------------------------ Starting model: R = 0.3746 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3302 (Rfree = 0.000) for 3420 atoms. Found 71 (71 requested) and removed 68 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.72 2.21 Round 1: 252 peptides, 36 chains. Longest chain 24 peptides. Score 0.487 Round 2: 261 peptides, 29 chains. Longest chain 27 peptides. Score 0.581 Round 3: 283 peptides, 24 chains. Longest chain 31 peptides. Score 0.671 Round 4: 292 peptides, 26 chains. Longest chain 28 peptides. Score 0.670 Round 5: 282 peptides, 22 chains. Longest chain 43 peptides. Score 0.687 Taking the results from Round 5 Chains 22, Residues 260, Estimated correctness of the model 85.3 % 6 chains (147 residues) have been docked in sequence ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 4670 restraints for refining 2973 atoms. 3066 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3056 (Rfree = 0.000) for 2973 atoms. Found 62 (62 requested) and removed 38 (31 requested) atoms. Cycle 2: After refmac, R = 0.2865 (Rfree = 0.000) for 2963 atoms. Found 61 (62 requested) and removed 35 (31 requested) atoms. Cycle 3: After refmac, R = 0.2744 (Rfree = 0.000) for 2973 atoms. Found 51 (62 requested) and removed 35 (31 requested) atoms. Cycle 4: After refmac, R = 0.2771 (Rfree = 0.000) for 2980 atoms. Found 38 (62 requested) and removed 39 (31 requested) atoms. Cycle 5: After refmac, R = 0.2684 (Rfree = 0.000) for 2973 atoms. Found 47 (62 requested) and removed 33 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.65 2.16 Round 1: 290 peptides, 22 chains. Longest chain 54 peptides. Score 0.700 Round 2: 308 peptides, 19 chains. Longest chain 69 peptides. Score 0.751 Round 3: 311 peptides, 20 chains. Longest chain 46 peptides. Score 0.748 Round 4: 311 peptides, 22 chains. Longest chain 37 peptides. Score 0.733 Round 5: 318 peptides, 15 chains. Longest chain 79 peptides. Score 0.792 Taking the results from Round 5 Chains 17, Residues 303, Estimated correctness of the model 93.0 % 7 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 51 A Built loop between residues 171 A and 179 A Built loop between residues 324 A and 327 A Built loop between residues 338 A and 341 A 12 chains (315 residues) following loop building 3 chains (260 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3466 restraints for refining 2991 atoms. 1185 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2715 (Rfree = 0.000) for 2991 atoms. Found 62 (62 requested) and removed 36 (31 requested) atoms. Cycle 7: After refmac, R = 0.2545 (Rfree = 0.000) for 3006 atoms. Found 61 (61 requested) and removed 36 (31 requested) atoms. Cycle 8: After refmac, R = 0.2474 (Rfree = 0.000) for 3024 atoms. Found 60 (60 requested) and removed 34 (31 requested) atoms. Cycle 9: After refmac, R = 0.2378 (Rfree = 0.000) for 3043 atoms. Found 59 (59 requested) and removed 39 (31 requested) atoms. Cycle 10: After refmac, R = 0.2387 (Rfree = 0.000) for 3057 atoms. Found 53 (58 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.65 2.16 Round 1: 313 peptides, 15 chains. Longest chain 51 peptides. Score 0.785 Round 2: 321 peptides, 15 chains. Longest chain 105 peptides. Score 0.795 Round 3: 321 peptides, 12 chains. Longest chain 124 peptides. Score 0.814 Round 4: 322 peptides, 20 chains. Longest chain 59 peptides. Score 0.763 Round 5: 319 peptides, 15 chains. Longest chain 55 peptides. Score 0.793 Taking the results from Round 3 Chains 14, Residues 309, Estimated correctness of the model 94.3 % 4 chains (237 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 131 A 12 chains (310 residues) following loop building 3 chains (239 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3602 restraints for refining 2912 atoms. 1425 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2505 (Rfree = 0.000) for 2912 atoms. Found 54 (54 requested) and removed 35 (30 requested) atoms. Cycle 12: After refmac, R = 0.2380 (Rfree = 0.000) for 2922 atoms. Found 54 (54 requested) and removed 32 (30 requested) atoms. Cycle 13: After refmac, R = 0.2336 (Rfree = 0.000) for 2942 atoms. Found 49 (52 requested) and removed 32 (30 requested) atoms. Cycle 14: After refmac, R = 0.2273 (Rfree = 0.000) for 2955 atoms. Found 48 (51 requested) and removed 31 (30 requested) atoms. Cycle 15: After refmac, R = 0.2242 (Rfree = 0.000) for 2966 atoms. Found 50 (50 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.67 2.17 Round 1: 318 peptides, 14 chains. Longest chain 69 peptides. Score 0.798 Round 2: 331 peptides, 13 chains. Longest chain 87 peptides. Score 0.819 Round 3: 330 peptides, 13 chains. Longest chain 76 peptides. Score 0.818 Round 4: 332 peptides, 15 chains. Longest chain 92 peptides. Score 0.808 Round 5: 321 peptides, 15 chains. Longest chain 76 peptides. Score 0.795 Taking the results from Round 2 Chains 15, Residues 318, Estimated correctness of the model 94.6 % 6 chains (271 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 49 A Built loop between residues 165 A and 169 A Built loop between residues 330 A and 333 A 11 chains (326 residues) following loop building 3 chains (280 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3252 restraints for refining 2935 atoms. 867 conditional restraints added. Observations/parameters ratio is 2.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2398 (Rfree = 0.000) for 2935 atoms. Found 49 (49 requested) and removed 34 (30 requested) atoms. Cycle 17: After refmac, R = 0.2258 (Rfree = 0.000) for 2945 atoms. Found 48 (48 requested) and removed 31 (30 requested) atoms. Cycle 18: After refmac, R = 0.2180 (Rfree = 0.000) for 2958 atoms. Found 46 (46 requested) and removed 30 (30 requested) atoms. Cycle 19: After refmac, R = 0.2145 (Rfree = 0.000) for 2972 atoms. Found 46 (46 requested) and removed 31 (31 requested) atoms. Cycle 20: After refmac, R = 0.2115 (Rfree = 0.000) for 2981 atoms. Found 42 (45 requested) and removed 32 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.67 2.17 Round 1: 326 peptides, 12 chains. Longest chain 87 peptides. Score 0.820 Round 2: 328 peptides, 11 chains. Longest chain 88 peptides. Score 0.828 Round 3: 319 peptides, 17 chains. Longest chain 67 peptides. Score 0.779 Round 4: 328 peptides, 15 chains. Longest chain 67 peptides. Score 0.803 Round 5: 327 peptides, 15 chains. Longest chain 70 peptides. Score 0.802 Taking the results from Round 2 Chains 16, Residues 317, Estimated correctness of the model 95.1 % 8 chains (294 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 50 A Built loop between residues 129 A and 132 A Built loop between residues 164 A and 169 A Built loop between residues 304 A and 313 A 11 chains (334 residues) following loop building 4 chains (312 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3227 restraints for refining 3034 atoms. 682 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2415 (Rfree = 0.000) for 3034 atoms. Found 44 (44 requested) and removed 35 (31 requested) atoms. Cycle 22: After refmac, R = 0.2247 (Rfree = 0.000) for 3035 atoms. Found 43 (43 requested) and removed 33 (31 requested) atoms. Cycle 23: After refmac, R = 0.2195 (Rfree = 0.000) for 3041 atoms. Found 42 (42 requested) and removed 31 (31 requested) atoms. Cycle 24: After refmac, R = 0.2134 (Rfree = 0.000) for 3048 atoms. Found 40 (40 requested) and removed 34 (31 requested) atoms. Cycle 25: After refmac, R = 0.2133 (Rfree = 0.000) for 3051 atoms. Found 39 (39 requested) and removed 32 (31 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.66 2.16 Round 1: 327 peptides, 12 chains. Longest chain 96 peptides. Score 0.821 Round 2: 325 peptides, 11 chains. Longest chain 93 peptides. Score 0.825 Round 3: 332 peptides, 12 chains. Longest chain 86 peptides. Score 0.826 Round 4: 328 peptides, 13 chains. Longest chain 79 peptides. Score 0.816 Round 5: 329 peptides, 11 chains. Longest chain 70 peptides. Score 0.829 Taking the results from Round 5 Chains 11, Residues 318, Estimated correctness of the model 95.1 % 8 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 46 A Built loop between residues 129 A and 132 A Built loop between residues 197 A and 200 A Built loop between residues 232 A and 235 A Built loop between residues 304 A and 310 A 6 chains (332 residues) following loop building 3 chains (305 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3305 restraints for refining 3027 atoms. 784 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2425 (Rfree = 0.000) for 3027 atoms. Found 38 (38 requested) and removed 37 (31 requested) atoms. Cycle 27: After refmac, R = 0.2269 (Rfree = 0.000) for 3021 atoms. Found 37 (37 requested) and removed 32 (31 requested) atoms. Cycle 28: After refmac, R = 0.2201 (Rfree = 0.000) for 3022 atoms. Found 35 (35 requested) and removed 34 (31 requested) atoms. Cycle 29: After refmac, R = 0.2174 (Rfree = 0.000) for 3020 atoms. Found 34 (34 requested) and removed 35 (31 requested) atoms. Cycle 30: After refmac, R = 0.2134 (Rfree = 0.000) for 3017 atoms. Found 32 (32 requested) and removed 34 (31 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.65 2.16 Round 1: 329 peptides, 11 chains. Longest chain 84 peptides. Score 0.829 Round 2: 335 peptides, 10 chains. Longest chain 116 peptides. Score 0.840 Round 3: 323 peptides, 16 chains. Longest chain 58 peptides. Score 0.791 Round 4: 325 peptides, 13 chains. Longest chain 86 peptides. Score 0.812 Round 5: 314 peptides, 13 chains. Longest chain 59 peptides. Score 0.800 Taking the results from Round 2 Chains 10, Residues 325, Estimated correctness of the model 95.7 % 6 chains (305 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 54 A Built loop between residues 137 A and 140 A Built loop between residues 304 A and 310 A 7 chains (334 residues) following loop building 3 chains (314 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3279 restraints for refining 3010 atoms. 716 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2379 (Rfree = 0.000) for 3010 atoms. Found 31 (31 requested) and removed 33 (31 requested) atoms. Cycle 32: After refmac, R = 0.2224 (Rfree = 0.000) for 3005 atoms. Found 31 (31 requested) and removed 32 (31 requested) atoms. Cycle 33: After refmac, R = 0.2161 (Rfree = 0.000) for 3002 atoms. Found 31 (31 requested) and removed 31 (31 requested) atoms. Cycle 34: After refmac, R = 0.2135 (Rfree = 0.000) for 2996 atoms. Found 31 (31 requested) and removed 33 (31 requested) atoms. Cycle 35: After refmac, R = 0.2116 (Rfree = 0.000) for 2993 atoms. Found 31 (31 requested) and removed 33 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.64 2.15 Round 1: 325 peptides, 11 chains. Longest chain 84 peptides. Score 0.825 Round 2: 328 peptides, 10 chains. Longest chain 122 peptides. Score 0.833 Round 3: 326 peptides, 10 chains. Longest chain 80 peptides. Score 0.832 Round 4: 327 peptides, 14 chains. Longest chain 73 peptides. Score 0.808 Round 5: 321 peptides, 13 chains. Longest chain 69 peptides. Score 0.808 Taking the results from Round 2 Chains 15, Residues 318, Estimated correctness of the model 95.3 % 9 chains (279 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 55 A Built loop between residues 99 A and 103 A Built loop between residues 166 A and 169 A Built loop between residues 304 A and 310 A Built loop between residues 339 A and 342 A 9 chains (333 residues) following loop building 4 chains (300 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3266 restraints for refining 2973 atoms. 788 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2465 (Rfree = 0.000) for 2973 atoms. Found 31 (31 requested) and removed 39 (31 requested) atoms. Cycle 37: After refmac, R = 0.2276 (Rfree = 0.000) for 2960 atoms. Found 30 (30 requested) and removed 31 (30 requested) atoms. Cycle 38: After refmac, R = 0.2209 (Rfree = 0.000) for 2958 atoms. Found 30 (30 requested) and removed 34 (30 requested) atoms. Cycle 39: After refmac, R = 0.2167 (Rfree = 0.000) for 2953 atoms. Found 30 (30 requested) and removed 31 (30 requested) atoms. Cycle 40: After refmac, R = 0.2163 (Rfree = 0.000) for 2951 atoms. Found 30 (30 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.65 2.16 Round 1: 322 peptides, 13 chains. Longest chain 57 peptides. Score 0.809 Round 2: 327 peptides, 13 chains. Longest chain 62 peptides. Score 0.815 Round 3: 325 peptides, 10 chains. Longest chain 135 peptides. Score 0.830 Round 4: 325 peptides, 12 chains. Longest chain 85 peptides. Score 0.818 Round 5: 322 peptides, 12 chains. Longest chain 70 peptides. Score 0.815 Taking the results from Round 3 Chains 14, Residues 315, Estimated correctness of the model 95.2 % 9 chains (282 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 50 A Built loop between residues 54 A and 57 A Built loop between residues 100 A and 104 A Built loop between residues 207 A and 214 A Built loop between residues 238 A and 241 A Built loop between residues 303 A and 310 A 5 chains (331 residues) following loop building 3 chains (305 residues) in sequence following loop building ------------------------------------------------------ 24667 reflections ( 99.85 % complete ) and 3264 restraints for refining 2975 atoms. 757 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2444 (Rfree = 0.000) for 2975 atoms. Found 31 (31 requested) and removed 40 (31 requested) atoms. Cycle 42: After refmac, R = 0.2275 (Rfree = 0.000) for 2962 atoms. Found 30 (30 requested) and removed 31 (30 requested) atoms. Cycle 43: After refmac, R = 0.2179 (Rfree = 0.000) for 2961 atoms. Found 30 (30 requested) and removed 30 (30 requested) atoms. Cycle 44: After refmac, R = 0.2124 (Rfree = 0.000) for 2961 atoms. Found 30 (30 requested) and removed 33 (30 requested) atoms. Cycle 45: After refmac, R = 0.2092 (Rfree = 0.000) for 2958 atoms. Found 30 (30 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.65 2.16 Round 1: 324 peptides, 13 chains. Longest chain 120 peptides. Score 0.811 Round 2: 336 peptides, 11 chains. Longest chain 119 peptides. Score 0.836 Round 3: 335 peptides, 11 chains. Longest chain 127 peptides. Score 0.835 Round 4: 330 peptides, 12 chains. Longest chain 74 peptides. Score 0.824 Round 5: 326 peptides, 12 chains. Longest chain 55 peptides. Score 0.820 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 325, Estimated correctness of the model 95.5 % 6 chains (293 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 205 A and 209 A Built loop between residues 302 A and 306 A Built loop between residues 339 A and 342 A 8 chains (333 residues) following loop building 3 chains (301 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 24667 reflections ( 99.85 % complete ) and 2496 restraints for refining 2448 atoms. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3054 (Rfree = 0.000) for 2448 atoms. Found 25 (25 requested) and removed 0 (25 requested) atoms. Cycle 47: After refmac, R = 0.2837 (Rfree = 0.000) for 2448 atoms. Found 25 (25 requested) and removed 3 (25 requested) atoms. Cycle 48: After refmac, R = 0.2749 (Rfree = 0.000) for 2448 atoms. Found 23 (26 requested) and removed 2 (26 requested) atoms. Cycle 49: After refmac, R = 0.2676 (Rfree = 0.000) for 2448 atoms. Found 7 (26 requested) and removed 6 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:28:31 GMT 2018 Job finished. TimeTaking 65.44 Used memory is bytes: 5392824