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 2a6a-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.2-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/2a6a-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.2-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/2a6a-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.2-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 339 and 0 Target number of residues in the AU: 339 Target solvent content: 0.6516 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-3.2-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3488 target number of atoms Had to go as low as 0.65 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: 108.588 3.200 Wilson plot Bfac: 79.01 9055 reflections ( 99.15 % complete ) and 0 restraints for refining 3873 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3392 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3366 (Rfree = 0.000) for 3873 atoms. Found 34 (34 requested) and removed 46 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.23 Search for helices and strands: 0 residues in 0 chains, 3930 seeds are put forward NCS extension: 0 residues added, 3930 seeds are put forward Round 1: 199 peptides, 34 chains. Longest chain 16 peptides. Score 0.387 Round 2: 225 peptides, 27 chains. Longest chain 18 peptides. Score 0.550 Round 3: 265 peptides, 31 chains. Longest chain 25 peptides. Score 0.602 Round 4: 262 peptides, 28 chains. Longest chain 45 peptides. Score 0.626 Round 5: 258 peptides, 30 chains. Longest chain 23 peptides. Score 0.596 Taking the results from Round 4 Chains 30, Residues 234, Estimated correctness of the model 47.9 % 1 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6709 restraints for refining 3185 atoms. 5666 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3094 (Rfree = 0.000) for 3185 atoms. Found 28 (28 requested) and removed 47 (14 requested) atoms. Cycle 2: After refmac, R = 0.2843 (Rfree = 0.000) for 3113 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. Cycle 3: After refmac, R = 0.2616 (Rfree = 0.000) for 3078 atoms. Found 14 (27 requested) and removed 19 (13 requested) atoms. Cycle 4: After refmac, R = 0.2688 (Rfree = 0.000) for 3057 atoms. Found 23 (27 requested) and removed 22 (13 requested) atoms. Cycle 5: After refmac, R = 0.2698 (Rfree = 0.000) for 3044 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3162 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3176 seeds are put forward Round 1: 226 peptides, 30 chains. Longest chain 24 peptides. Score 0.517 Round 2: 266 peptides, 30 chains. Longest chain 42 peptides. Score 0.614 Round 3: 268 peptides, 26 chains. Longest chain 32 peptides. Score 0.658 Round 4: 274 peptides, 25 chains. Longest chain 26 peptides. Score 0.680 Round 5: 278 peptides, 25 chains. Longest chain 38 peptides. Score 0.687 Taking the results from Round 5 Chains 26, Residues 253, Estimated correctness of the model 62.4 % 2 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6305 restraints for refining 3156 atoms. 5136 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3137 (Rfree = 0.000) for 3156 atoms. Found 28 (28 requested) and removed 51 (14 requested) atoms. Cycle 7: After refmac, R = 0.2735 (Rfree = 0.000) for 3088 atoms. Found 25 (28 requested) and removed 27 (14 requested) atoms. Cycle 8: After refmac, R = 0.2647 (Rfree = 0.000) for 3054 atoms. Found 26 (27 requested) and removed 21 (13 requested) atoms. Cycle 9: After refmac, R = 0.2530 (Rfree = 0.000) for 3040 atoms. Found 24 (27 requested) and removed 23 (13 requested) atoms. Cycle 10: After refmac, R = 0.2763 (Rfree = 0.000) for 3025 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3146 seeds are put forward NCS extension: 51 residues added (1 deleted due to clashes), 3197 seeds are put forward Round 1: 245 peptides, 33 chains. Longest chain 31 peptides. Score 0.531 Round 2: 269 peptides, 24 chains. Longest chain 33 peptides. Score 0.679 Round 3: 262 peptides, 28 chains. Longest chain 37 peptides. Score 0.626 Round 4: 273 peptides, 30 chains. Longest chain 26 peptides. Score 0.630 Round 5: 288 peptides, 33 chains. Longest chain 26 peptides. Score 0.632 Taking the results from Round 2 Chains 28, Residues 245, Estimated correctness of the model 60.6 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 5936 restraints for refining 3053 atoms. 4776 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2793 (Rfree = 0.000) for 3053 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 12: After refmac, R = 0.2391 (Rfree = 0.000) for 3031 atoms. Found 24 (27 requested) and removed 19 (13 requested) atoms. Cycle 13: After refmac, R = 0.2325 (Rfree = 0.000) for 3011 atoms. Found 20 (27 requested) and removed 18 (13 requested) atoms. Cycle 14: After refmac, R = 0.2668 (Rfree = 0.000) for 3004 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 15: After refmac, R = 0.2635 (Rfree = 0.000) for 2976 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3080 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 3118 seeds are put forward Round 1: 233 peptides, 31 chains. Longest chain 20 peptides. Score 0.523 Round 2: 260 peptides, 30 chains. Longest chain 23 peptides. Score 0.601 Round 3: 271 peptides, 28 chains. Longest chain 32 peptides. Score 0.645 Round 4: 261 peptides, 29 chains. Longest chain 22 peptides. Score 0.613 Round 5: 264 peptides, 27 chains. Longest chain 22 peptides. Score 0.640 Taking the results from Round 3 Chains 28, Residues 243, Estimated correctness of the model 52.6 % 4 chains (78 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 5668 restraints for refining 3075 atoms. 4439 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2717 (Rfree = 0.000) for 3075 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 17: After refmac, R = 0.2405 (Rfree = 0.000) for 3045 atoms. Found 20 (27 requested) and removed 26 (13 requested) atoms. Cycle 18: After refmac, R = 0.2265 (Rfree = 0.000) for 3021 atoms. Found 10 (27 requested) and removed 24 (13 requested) atoms. Cycle 19: After refmac, R = 0.2270 (Rfree = 0.000) for 2999 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 20: After refmac, R = 0.2226 (Rfree = 0.000) for 2999 atoms. Found 20 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3104 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 3128 seeds are put forward Round 1: 231 peptides, 31 chains. Longest chain 19 peptides. Score 0.518 Round 2: 263 peptides, 28 chains. Longest chain 30 peptides. Score 0.628 Round 3: 288 peptides, 29 chains. Longest chain 31 peptides. Score 0.670 Round 4: 273 peptides, 32 chains. Longest chain 29 peptides. Score 0.609 Round 5: 284 peptides, 25 chains. Longest chain 47 peptides. Score 0.699 Taking the results from Round 5 Chains 28, Residues 259, Estimated correctness of the model 65.0 % 3 chains (71 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6015 restraints for refining 3184 atoms. 4754 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2822 (Rfree = 0.000) for 3184 atoms. Found 28 (28 requested) and removed 36 (14 requested) atoms. Cycle 22: After refmac, R = 0.2772 (Rfree = 0.000) for 3161 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 23: After refmac, R = 0.2355 (Rfree = 0.000) for 3128 atoms. Found 25 (28 requested) and removed 24 (14 requested) atoms. Cycle 24: After refmac, R = 0.2348 (Rfree = 0.000) for 3109 atoms. Found 16 (28 requested) and removed 21 (14 requested) atoms. Cycle 25: After refmac, R = 0.2598 (Rfree = 0.000) for 3089 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 3182 seeds are put forward NCS extension: 28 residues added (19 deleted due to clashes), 3210 seeds are put forward Round 1: 267 peptides, 33 chains. Longest chain 29 peptides. Score 0.585 Round 2: 281 peptides, 29 chains. Longest chain 46 peptides. Score 0.656 Round 3: 278 peptides, 29 chains. Longest chain 29 peptides. Score 0.650 Round 4: 272 peptides, 23 chains. Longest chain 51 peptides. Score 0.694 Round 5: 291 peptides, 30 chains. Longest chain 36 peptides. Score 0.667 Taking the results from Round 4 Chains 25, Residues 249, Estimated correctness of the model 63.9 % 2 chains (69 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6005 restraints for refining 3185 atoms. 4742 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3093 (Rfree = 0.000) for 3185 atoms. Found 28 (28 requested) and removed 56 (14 requested) atoms. Cycle 27: After refmac, R = 0.2500 (Rfree = 0.000) for 3136 atoms. Found 16 (28 requested) and removed 31 (14 requested) atoms. Cycle 28: After refmac, R = 0.2937 (Rfree = 0.000) for 3099 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 29: After refmac, R = 0.2454 (Rfree = 0.000) for 3092 atoms. Found 20 (27 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.2875 (Rfree = 0.000) for 3081 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3187 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3203 seeds are put forward Round 1: 223 peptides, 31 chains. Longest chain 23 peptides. Score 0.496 Round 2: 253 peptides, 29 chains. Longest chain 25 peptides. Score 0.595 Round 3: 264 peptides, 28 chains. Longest chain 24 peptides. Score 0.630 Round 4: 251 peptides, 26 chains. Longest chain 29 peptides. Score 0.622 Round 5: 262 peptides, 28 chains. Longest chain 29 peptides. Score 0.626 Taking the results from Round 3 Chains 30, Residues 236, Estimated correctness of the model 48.9 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6348 restraints for refining 3102 atoms. 5369 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2623 (Rfree = 0.000) for 3102 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 32: After refmac, R = 0.2803 (Rfree = 0.000) for 3084 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 33: After refmac, R = 0.2736 (Rfree = 0.000) for 3076 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 34: After refmac, R = 0.2401 (Rfree = 0.000) for 3074 atoms. Found 19 (27 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.2361 (Rfree = 0.000) for 3073 atoms. Found 18 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3122 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 3155 seeds are put forward Round 1: 223 peptides, 31 chains. Longest chain 21 peptides. Score 0.496 Round 2: 244 peptides, 29 chains. Longest chain 21 peptides. Score 0.574 Round 3: 243 peptides, 27 chains. Longest chain 21 peptides. Score 0.593 Round 4: 266 peptides, 28 chains. Longest chain 24 peptides. Score 0.635 Round 5: 254 peptides, 28 chains. Longest chain 22 peptides. Score 0.608 Taking the results from Round 4 Chains 33, Residues 238, Estimated correctness of the model 50.2 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6351 restraints for refining 3132 atoms. 5345 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2595 (Rfree = 0.000) for 3132 atoms. Found 22 (28 requested) and removed 34 (14 requested) atoms. Cycle 37: After refmac, R = 0.2564 (Rfree = 0.000) for 3100 atoms. Found 23 (27 requested) and removed 24 (13 requested) atoms. Cycle 38: After refmac, R = 0.2889 (Rfree = 0.000) for 3090 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 39: After refmac, R = 0.2393 (Rfree = 0.000) for 3070 atoms. Found 24 (27 requested) and removed 19 (13 requested) atoms. Cycle 40: After refmac, R = 0.2706 (Rfree = 0.000) for 3066 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 3151 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3171 seeds are put forward Round 1: 233 peptides, 29 chains. Longest chain 27 peptides. Score 0.547 Round 2: 255 peptides, 28 chains. Longest chain 28 peptides. Score 0.610 Round 3: 254 peptides, 28 chains. Longest chain 29 peptides. Score 0.608 Round 4: 255 peptides, 31 chains. Longest chain 21 peptides. Score 0.578 Round 5: 261 peptides, 30 chains. Longest chain 29 peptides. Score 0.603 Taking the results from Round 2 Chains 30, Residues 227, Estimated correctness of the model 43.7 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6353 restraints for refining 3141 atoms. 5395 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2640 (Rfree = 0.000) for 3141 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 42: After refmac, R = 0.2905 (Rfree = 0.000) for 3125 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. Cycle 43: After refmac, R = 0.2419 (Rfree = 0.000) for 3111 atoms. Found 27 (28 requested) and removed 23 (14 requested) atoms. Cycle 44: After refmac, R = 0.2273 (Rfree = 0.000) for 3101 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. Cycle 45: After refmac, R = 0.2363 (Rfree = 0.000) for 3104 atoms. Found 19 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 3206 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3222 seeds are put forward Round 1: 213 peptides, 32 chains. Longest chain 20 peptides. Score 0.456 Round 2: 239 peptides, 30 chains. Longest chain 27 peptides. Score 0.550 Round 3: 242 peptides, 30 chains. Longest chain 24 peptides. Score 0.558 Round 4: 233 peptides, 28 chains. Longest chain 23 peptides. Score 0.558 Round 5: 244 peptides, 30 chains. Longest chain 23 peptides. Score 0.563 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 214, Estimated correctness of the model 30.7 % 3 chains (46 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 2a6a-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (214 residues) following loop building 3 chains (46 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9055 reflections ( 99.15 % complete ) and 6398 restraints for refining 3185 atoms. 5427 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2773 (Rfree = 0.000) for 3185 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2855 (Rfree = 0.000) for 3144 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2819 (Rfree = 0.000) for 3107 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2260 (Rfree = 0.000) for 3082 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:24:08 GMT 2018 Job finished. TimeTaking 61.06 Used memory is bytes: 18380680