null Mon 24 Dec 00:17:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p7i-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:17:45 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-4.0-parrot-mrncs/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 330 and 0 Target number of residues in the AU: 330 Target solvent content: 0.6733 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.51 Input MTZ file: 2p7i-4.0-parrot-mrncs.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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 4.000 Wilson plot Bfac: 95.23 4940 reflections ( 99.60 % complete ) and 0 restraints for refining 4411 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3402 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3477 (Rfree = 0.000) for 4411 atoms. Found 18 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 3.93 Search for helices and strands: 0 residues in 0 chains, 4499 seeds are put forward NCS extension: 0 residues added, 4499 seeds are put forward Round 1: 151 peptides, 33 chains. Longest chain 7 peptides. Score 0.237 Round 2: 214 peptides, 36 chains. Longest chain 16 peptides. Score 0.400 Round 3: 235 peptides, 33 chains. Longest chain 22 peptides. Score 0.496 Round 4: 243 peptides, 36 chains. Longest chain 17 peptides. Score 0.482 Round 5: 251 peptides, 37 chains. Longest chain 15 peptides. Score 0.492 Taking the results from Round 3 Chains 33, Residues 202, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 8390 restraints for refining 3575 atoms. 7573 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3063 (Rfree = 0.000) for 3575 atoms. Found 7 (16 requested) and removed 20 (8 requested) atoms. Cycle 2: After refmac, R = 0.2768 (Rfree = 0.000) for 3484 atoms. Found 13 (16 requested) and removed 22 (8 requested) atoms. Cycle 3: After refmac, R = 0.2438 (Rfree = 0.000) for 3439 atoms. Found 3 (16 requested) and removed 22 (8 requested) atoms. Cycle 4: After refmac, R = 0.2296 (Rfree = 0.000) for 3399 atoms. Found 4 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2549 (Rfree = 0.000) for 3375 atoms. Found 8 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.75 Search for helices and strands: 0 residues in 0 chains, 3489 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 3521 seeds are put forward Round 1: 190 peptides, 33 chains. Longest chain 12 peptides. Score 0.367 Round 2: 245 peptides, 40 chains. Longest chain 17 peptides. Score 0.440 Round 3: 251 peptides, 34 chains. Longest chain 17 peptides. Score 0.526 Round 4: 249 peptides, 36 chains. Longest chain 14 peptides. Score 0.498 Round 5: 225 peptides, 30 chains. Longest chain 23 peptides. Score 0.505 Taking the results from Round 3 Chains 35, Residues 217, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 7754 restraints for refining 3459 atoms. 6871 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2718 (Rfree = 0.000) for 3459 atoms. Found 10 (16 requested) and removed 31 (8 requested) atoms. Cycle 7: After refmac, R = 0.2521 (Rfree = 0.000) for 3403 atoms. Found 13 (16 requested) and removed 20 (8 requested) atoms. Cycle 8: After refmac, R = 0.2487 (Rfree = 0.000) for 3363 atoms. Found 8 (16 requested) and removed 23 (8 requested) atoms. Cycle 9: After refmac, R = 0.2445 (Rfree = 0.000) for 3321 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2451 (Rfree = 0.000) for 3295 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 3388 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3405 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 12 peptides. Score 0.342 Round 2: 224 peptides, 36 chains. Longest chain 11 peptides. Score 0.429 Round 3: 249 peptides, 35 chains. Longest chain 16 peptides. Score 0.509 Round 4: 241 peptides, 38 chains. Longest chain 17 peptides. Score 0.453 Round 5: 253 peptides, 36 chains. Longest chain 17 peptides. Score 0.508 Taking the results from Round 3 Chains 35, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 7843 restraints for refining 3462 atoms. 7022 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2627 (Rfree = 0.000) for 3462 atoms. Found 15 (16 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.2629 (Rfree = 0.000) for 3423 atoms. Found 16 (16 requested) and removed 100 (8 requested) atoms. Cycle 13: After refmac, R = 0.2646 (Rfree = 0.000) for 3304 atoms. Found 11 (15 requested) and removed 22 (7 requested) atoms. Cycle 14: After refmac, R = 0.2442 (Rfree = 0.000) for 3273 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.2214 (Rfree = 0.000) for 3254 atoms. Found 3 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.76 Search for helices and strands: 0 residues in 0 chains, 3402 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3423 seeds are put forward Round 1: 183 peptides, 35 chains. Longest chain 10 peptides. Score 0.318 Round 2: 220 peptides, 36 chains. Longest chain 17 peptides. Score 0.418 Round 3: 216 peptides, 35 chains. Longest chain 12 peptides. Score 0.419 Round 4: 211 peptides, 28 chains. Longest chain 18 peptides. Score 0.492 Round 5: 199 peptides, 33 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 4 Chains 28, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 7636 restraints for refining 3361 atoms. 6932 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2904 (Rfree = 0.000) for 3361 atoms. Found 14 (15 requested) and removed 26 (7 requested) atoms. Cycle 17: After refmac, R = 0.2873 (Rfree = 0.000) for 3313 atoms. Found 8 (15 requested) and removed 25 (7 requested) atoms. Cycle 18: After refmac, R = 0.2796 (Rfree = 0.000) for 3281 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 19: After refmac, R = 0.2944 (Rfree = 0.000) for 3262 atoms. Found 12 (15 requested) and removed 20 (7 requested) atoms. Cycle 20: After refmac, R = 0.2836 (Rfree = 0.000) for 3240 atoms. Found 12 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.89 3.84 Search for helices and strands: 0 residues in 0 chains, 3384 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3402 seeds are put forward Round 1: 183 peptides, 37 chains. Longest chain 8 peptides. Score 0.290 Round 2: 194 peptides, 33 chains. Longest chain 13 peptides. Score 0.380 Round 3: 204 peptides, 32 chains. Longest chain 16 peptides. Score 0.423 Round 4: 210 peptides, 35 chains. Longest chain 17 peptides. Score 0.401 Round 5: 206 peptides, 34 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 3 Chains 32, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 7369 restraints for refining 3277 atoms. 6713 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2897 (Rfree = 0.000) for 3277 atoms. Found 12 (15 requested) and removed 25 (7 requested) atoms. Cycle 22: After refmac, R = 0.2861 (Rfree = 0.000) for 3239 atoms. Found 10 (15 requested) and removed 19 (7 requested) atoms. Cycle 23: After refmac, R = 0.2746 (Rfree = 0.000) for 3213 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 24: After refmac, R = 0.2741 (Rfree = 0.000) for 3184 atoms. Found 10 (15 requested) and removed 27 (7 requested) atoms. Cycle 25: After refmac, R = 0.2472 (Rfree = 0.000) for 3156 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 3306 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3323 seeds are put forward Round 1: 161 peptides, 34 chains. Longest chain 8 peptides. Score 0.258 Round 2: 198 peptides, 35 chains. Longest chain 11 peptides. Score 0.365 Round 3: 193 peptides, 36 chains. Longest chain 11 peptides. Score 0.336 Round 4: 203 peptides, 36 chains. Longest chain 12 peptides. Score 0.367 Round 5: 200 peptides, 34 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 5 Chains 34, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 7338 restraints for refining 3284 atoms. 6708 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3036 (Rfree = 0.000) for 3284 atoms. Found 13 (15 requested) and removed 27 (7 requested) atoms. Cycle 27: After refmac, R = 0.2800 (Rfree = 0.000) for 3246 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 28: After refmac, R = 0.2760 (Rfree = 0.000) for 3225 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. Cycle 29: After refmac, R = 0.2631 (Rfree = 0.000) for 3205 atoms. Found 13 (15 requested) and removed 13 (7 requested) atoms. Cycle 30: After refmac, R = 0.2612 (Rfree = 0.000) for 3196 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 3314 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3340 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 7 peptides. Score 0.254 Round 2: 200 peptides, 40 chains. Longest chain 11 peptides. Score 0.304 Round 3: 207 peptides, 37 chains. Longest chain 11 peptides. Score 0.366 Round 4: 214 peptides, 38 chains. Longest chain 14 peptides. Score 0.375 Round 5: 217 peptides, 36 chains. Longest chain 16 peptides. Score 0.409 Taking the results from Round 5 Chains 36, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 7729 restraints for refining 3403 atoms. 7041 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2741 (Rfree = 0.000) for 3403 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 32: After refmac, R = 0.2671 (Rfree = 0.000) for 3350 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 33: After refmac, R = 0.2634 (Rfree = 0.000) for 3327 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 34: After refmac, R = 0.2664 (Rfree = 0.000) for 3304 atoms. Found 13 (15 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.2562 (Rfree = 0.000) for 3291 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.72 Search for helices and strands: 0 residues in 0 chains, 3423 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3436 seeds are put forward Round 1: 131 peptides, 30 chains. Longest chain 6 peptides. Score 0.210 Round 2: 152 peptides, 31 chains. Longest chain 9 peptides. Score 0.271 Round 3: 170 peptides, 30 chains. Longest chain 10 peptides. Score 0.345 Round 4: 174 peptides, 34 chains. Longest chain 9 peptides. Score 0.302 Round 5: 173 peptides, 34 chains. Longest chain 8 peptides. Score 0.299 Taking the results from Round 3 Chains 30, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 7050 restraints for refining 3162 atoms. 6520 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2766 (Rfree = 0.000) for 3162 atoms. Found 13 (15 requested) and removed 19 (7 requested) atoms. Cycle 37: After refmac, R = 0.2939 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 38: After refmac, R = 0.2797 (Rfree = 0.000) for 3124 atoms. Found 12 (14 requested) and removed 16 (7 requested) atoms. Cycle 39: After refmac, R = 0.2814 (Rfree = 0.000) for 3104 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 40: After refmac, R = 0.2751 (Rfree = 0.000) for 3090 atoms. Found 11 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.73 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3204 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 7 peptides. Score 0.219 Round 2: 164 peptides, 33 chains. Longest chain 10 peptides. Score 0.283 Round 3: 160 peptides, 32 chains. Longest chain 11 peptides. Score 0.284 Round 4: 174 peptides, 32 chains. Longest chain 11 peptides. Score 0.330 Round 5: 162 peptides, 30 chains. Longest chain 11 peptides. Score 0.319 Taking the results from Round 4 Chains 32, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4940 reflections ( 99.60 % complete ) and 6742 restraints for refining 3068 atoms. 6206 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3003 (Rfree = 0.000) for 3068 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 42: After refmac, R = 0.2888 (Rfree = 0.000) for 3026 atoms. Found 11 (14 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.3000 (Rfree = 0.000) for 3005 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.2851 (Rfree = 0.000) for 2990 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 45: After refmac, R = 0.2486 (Rfree = 0.000) for 2981 atoms. Found 4 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.73 Search for helices and strands: 0 residues in 0 chains, 3065 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3073 seeds are put forward Round 1: 123 peptides, 26 chains. Longest chain 7 peptides. Score 0.242 Round 2: 126 peptides, 24 chains. Longest chain 9 peptides. Score 0.285 Round 3: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.269 Round 4: 118 peptides, 22 chains. Longest chain 8 peptides. Score 0.287 Round 5: 126 peptides, 23 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2p7i-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4940 reflections ( 99.60 % complete ) and 6467 restraints for refining 2917 atoms. 6078 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2946 (Rfree = 0.000) for 2917 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2872 (Rfree = 0.000) for 2895 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2896 (Rfree = 0.000) for 2885 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2866 (Rfree = 0.000) for 2862 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:58:11 GMT 2018 Job finished. TimeTaking 40.5 Used memory is bytes: 20695648