Mon 24 Dec 07:29:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pbl-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-parrot-noncs ############### 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 07:29:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-parrot-noncs/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 689 and 0 Target number of residues in the AU: 689 Target solvent content: 0.6307 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-3.6-parrot-noncs.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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.70 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: 87.858 3.600 Wilson plot Bfac: 66.84 11642 reflections ( 99.06 % complete ) and 0 restraints for refining 9290 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3535 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4137 (Rfree = 0.000) for 9290 atoms. Found 59 (59 requested) and removed 80 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 9461 seeds are put forward NCS extension: 0 residues added, 9461 seeds are put forward Round 1: 314 peptides, 68 chains. Longest chain 10 peptides. Score 0.248 Round 2: 455 peptides, 86 chains. Longest chain 13 peptides. Score 0.362 Round 3: 493 peptides, 90 chains. Longest chain 13 peptides. Score 0.396 Round 4: 490 peptides, 90 chains. Longest chain 13 peptides. Score 0.391 Round 5: 520 peptides, 89 chains. Longest chain 12 peptides. Score 0.443 Taking the results from Round 5 Chains 89, Residues 431, Estimated correctness of the model 0.0 % 16 chains (77 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16804 restraints for refining 7598 atoms. 14965 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3504 (Rfree = 0.000) for 7598 atoms. Found 48 (48 requested) and removed 76 (24 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.3419 (Rfree = 0.000) for 7387 atoms. Found 48 (48 requested) and removed 55 (24 requested) atoms. Cycle 3: After refmac, R = 0.3492 (Rfree = 0.000) for 7279 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. Cycle 4: After refmac, R = 0.3397 (Rfree = 0.000) for 7205 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. Cycle 5: After refmac, R = 0.3366 (Rfree = 0.000) for 7173 atoms. Found 46 (46 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 7506 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7519 seeds are put forward Round 1: 466 peptides, 94 chains. Longest chain 11 peptides. Score 0.325 Round 2: 502 peptides, 91 chains. Longest chain 14 peptides. Score 0.403 Round 3: 548 peptides, 92 chains. Longest chain 13 peptides. Score 0.465 Round 4: 556 peptides, 85 chains. Longest chain 15 peptides. Score 0.518 Round 5: 554 peptides, 89 chains. Longest chain 13 peptides. Score 0.492 Taking the results from Round 4 Chains 87, Residues 471, Estimated correctness of the model 0.0 % 10 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16542 restraints for refining 7428 atoms. 14569 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3197 (Rfree = 0.000) for 7428 atoms. Found 47 (47 requested) and removed 99 (23 requested) atoms. Cycle 7: After refmac, R = 0.2992 (Rfree = 0.000) for 7253 atoms. Found 47 (47 requested) and removed 62 (23 requested) atoms. Cycle 8: After refmac, R = 0.2712 (Rfree = 0.000) for 7196 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Cycle 9: After refmac, R = 0.2699 (Rfree = 0.000) for 7173 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. Cycle 10: After refmac, R = 0.2651 (Rfree = 0.000) for 7165 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.58 Search for helices and strands: 0 residues in 0 chains, 7515 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7531 seeds are put forward Round 1: 460 peptides, 88 chains. Longest chain 11 peptides. Score 0.357 Round 2: 513 peptides, 84 chains. Longest chain 14 peptides. Score 0.464 Round 3: 541 peptides, 88 chains. Longest chain 12 peptides. Score 0.480 Round 4: 544 peptides, 81 chains. Longest chain 16 peptides. Score 0.525 Round 5: 529 peptides, 86 chains. Longest chain 15 peptides. Score 0.475 Taking the results from Round 4 Chains 81, Residues 463, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 17056 restraints for refining 7525 atoms. 15254 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2928 (Rfree = 0.000) for 7525 atoms. Found 48 (48 requested) and removed 70 (24 requested) atoms. Cycle 12: After refmac, R = 0.2786 (Rfree = 0.000) for 7441 atoms. Found 48 (48 requested) and removed 54 (24 requested) atoms. Cycle 13: After refmac, R = 0.2719 (Rfree = 0.000) for 7391 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. Cycle 14: After refmac, R = 0.2608 (Rfree = 0.000) for 7378 atoms. Found 47 (47 requested) and removed 32 (23 requested) atoms. Cycle 15: After refmac, R = 0.2584 (Rfree = 0.000) for 7376 atoms. Found 47 (47 requested) and removed 40 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 7728 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 7743 seeds are put forward Round 1: 413 peptides, 82 chains. Longest chain 11 peptides. Score 0.320 Round 2: 510 peptides, 88 chains. Longest chain 15 peptides. Score 0.435 Round 3: 494 peptides, 78 chains. Longest chain 15 peptides. Score 0.474 Round 4: 487 peptides, 76 chains. Longest chain 13 peptides. Score 0.477 Round 5: 492 peptides, 74 chains. Longest chain 19 peptides. Score 0.496 Taking the results from Round 5 Chains 76, Residues 418, Estimated correctness of the model 0.0 % 7 chains (53 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 17184 restraints for refining 7599 atoms. 15375 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3085 (Rfree = 0.000) for 7599 atoms. Found 48 (48 requested) and removed 78 (24 requested) atoms. Cycle 17: After refmac, R = 0.2972 (Rfree = 0.000) for 7487 atoms. Found 48 (48 requested) and removed 49 (24 requested) atoms. Cycle 18: After refmac, R = 0.2829 (Rfree = 0.000) for 7445 atoms. Found 48 (48 requested) and removed 38 (24 requested) atoms. Cycle 19: After refmac, R = 0.2112 (Rfree = 0.000) for 7417 atoms. Found 47 (47 requested) and removed 28 (23 requested) atoms. Cycle 20: After refmac, R = 0.1825 (Rfree = 0.000) for 7416 atoms. Found 25 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 7662 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7680 seeds are put forward Round 1: 413 peptides, 86 chains. Longest chain 11 peptides. Score 0.292 Round 2: 490 peptides, 84 chains. Longest chain 13 peptides. Score 0.430 Round 3: 494 peptides, 80 chains. Longest chain 20 peptides. Score 0.462 Round 4: 490 peptides, 75 chains. Longest chain 14 peptides. Score 0.487 Round 5: 525 peptides, 82 chains. Longest chain 14 peptides. Score 0.494 Taking the results from Round 5 Chains 83, Residues 443, Estimated correctness of the model 0.0 % 8 chains (40 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 17093 restraints for refining 7600 atoms. 15292 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3179 (Rfree = 0.000) for 7600 atoms. Found 48 (48 requested) and removed 63 (24 requested) atoms. Cycle 22: After refmac, R = 0.3012 (Rfree = 0.000) for 7485 atoms. Found 48 (48 requested) and removed 48 (24 requested) atoms. Cycle 23: After refmac, R = 0.2863 (Rfree = 0.000) for 7426 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 24: After refmac, R = 0.2815 (Rfree = 0.000) for 7411 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 25: After refmac, R = 0.2125 (Rfree = 0.000) for 7397 atoms. Found 42 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.67 Search for helices and strands: 0 residues in 0 chains, 7683 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 7696 seeds are put forward Round 1: 407 peptides, 85 chains. Longest chain 11 peptides. Score 0.289 Round 2: 459 peptides, 82 chains. Longest chain 12 peptides. Score 0.396 Round 3: 447 peptides, 76 chains. Longest chain 14 peptides. Score 0.417 Round 4: 463 peptides, 73 chains. Longest chain 15 peptides. Score 0.461 Round 5: 472 peptides, 75 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 5 Chains 75, Residues 397, Estimated correctness of the model 0.0 % 9 chains (39 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 17159 restraints for refining 7489 atoms. 15555 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3069 (Rfree = 0.000) for 7489 atoms. Found 48 (48 requested) and removed 61 (24 requested) atoms. Cycle 27: After refmac, R = 0.3141 (Rfree = 0.000) for 7404 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 28: After refmac, R = 0.2943 (Rfree = 0.000) for 7358 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. Cycle 29: After refmac, R = 0.2940 (Rfree = 0.000) for 7326 atoms. Found 47 (47 requested) and removed 33 (23 requested) atoms. Cycle 30: After refmac, R = 0.2940 (Rfree = 0.000) for 7309 atoms. Found 47 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.63 Search for helices and strands: 0 residues in 0 chains, 7577 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7593 seeds are put forward Round 1: 347 peptides, 69 chains. Longest chain 11 peptides. Score 0.301 Round 2: 414 peptides, 73 chains. Longest chain 22 peptides. Score 0.385 Round 3: 428 peptides, 75 chains. Longest chain 17 peptides. Score 0.394 Round 4: 438 peptides, 78 chains. Longest chain 13 peptides. Score 0.389 Round 5: 439 peptides, 71 chains. Longest chain 17 peptides. Score 0.438 Taking the results from Round 5 Chains 72, Residues 368, Estimated correctness of the model 0.0 % 8 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16290 restraints for refining 7385 atoms. 14677 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3190 (Rfree = 0.000) for 7385 atoms. Found 47 (47 requested) and removed 67 (23 requested) atoms. Cycle 32: After refmac, R = 0.2990 (Rfree = 0.000) for 7296 atoms. Found 47 (47 requested) and removed 40 (23 requested) atoms. Cycle 33: After refmac, R = 0.3040 (Rfree = 0.000) for 7251 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. Cycle 34: After refmac, R = 0.2962 (Rfree = 0.000) for 7222 atoms. Found 46 (46 requested) and removed 31 (23 requested) atoms. Cycle 35: After refmac, R = 0.2820 (Rfree = 0.000) for 7213 atoms. Found 46 (46 requested) and removed 35 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 7437 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7455 seeds are put forward Round 1: 313 peptides, 62 chains. Longest chain 12 peptides. Score 0.293 Round 2: 358 peptides, 66 chains. Longest chain 10 peptides. Score 0.342 Round 3: 398 peptides, 66 chains. Longest chain 14 peptides. Score 0.408 Round 4: 376 peptides, 66 chains. Longest chain 12 peptides. Score 0.372 Round 5: 405 peptides, 65 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 5 Chains 66, Residues 340, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16254 restraints for refining 7261 atoms. 14864 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3077 (Rfree = 0.000) for 7261 atoms. Found 46 (46 requested) and removed 53 (23 requested) atoms. Cycle 37: After refmac, R = 0.2962 (Rfree = 0.000) for 7184 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. Cycle 38: After refmac, R = 0.3013 (Rfree = 0.000) for 7163 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. Cycle 39: After refmac, R = 0.2977 (Rfree = 0.000) for 7148 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. Cycle 40: After refmac, R = 0.2154 (Rfree = 0.000) for 7140 atoms. Found 45 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 7373 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 7382 seeds are put forward Round 1: 271 peptides, 58 chains. Longest chain 9 peptides. Score 0.246 Round 2: 303 peptides, 55 chains. Longest chain 12 peptides. Score 0.329 Round 3: 321 peptides, 57 chains. Longest chain 18 peptides. Score 0.345 Round 4: 339 peptides, 56 chains. Longest chain 16 peptides. Score 0.383 Round 5: 332 peptides, 57 chains. Longest chain 15 peptides. Score 0.364 Taking the results from Round 4 Chains 58, Residues 283, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 15914 restraints for refining 7042 atoms. 14749 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2955 (Rfree = 0.000) for 7042 atoms. Found 45 (45 requested) and removed 53 (22 requested) atoms. Cycle 42: After refmac, R = 0.2887 (Rfree = 0.000) for 7001 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 43: After refmac, R = 0.2898 (Rfree = 0.000) for 6969 atoms. Found 44 (44 requested) and removed 29 (22 requested) atoms. Cycle 44: After refmac, R = 0.2868 (Rfree = 0.000) for 6964 atoms. Found 44 (44 requested) and removed 30 (22 requested) atoms. Cycle 45: After refmac, R = 0.2041 (Rfree = 0.000) for 6961 atoms. Found 44 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 7142 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7155 seeds are put forward Round 1: 274 peptides, 57 chains. Longest chain 10 peptides. Score 0.260 Round 2: 329 peptides, 60 chains. Longest chain 14 peptides. Score 0.337 Round 3: 329 peptides, 57 chains. Longest chain 18 peptides. Score 0.359 Round 4: 315 peptides, 56 chains. Longest chain 19 peptides. Score 0.342 Round 5: 307 peptides, 51 chains. Longest chain 18 peptides. Score 0.367 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 256, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (256 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11642 reflections ( 99.06 % complete ) and 15596 restraints for refining 6848 atoms. 14615 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2940 (Rfree = 0.000) for 6848 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.3088 (Rfree = 0.000) for 6804 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2989 (Rfree = 0.000) for 6759 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.3099 (Rfree = 0.000) for 6726 atoms. TimeTaking 75.07