Mon 24 Dec 07:57:05 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 2hx1-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-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/2hx1-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-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 07:57:10 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/2hx1-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-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 800 and 0 Target number of residues in the AU: 800 Target solvent content: 0.6349 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-4.0-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: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.75 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: 93.753 4.000 Wilson plot Bfac: 69.10 10515 reflections ( 99.59 % complete ) and 0 restraints for refining 10113 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3487 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3495 (Rfree = 0.000) for 10113 atoms. Found 48 (48 requested) and removed 45 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 10312 seeds are put forward NCS extension: 0 residues added, 10312 seeds are put forward Round 1: 363 peptides, 75 chains. Longest chain 9 peptides. Score 0.271 Round 2: 524 peptides, 92 chains. Longest chain 15 peptides. Score 0.400 Round 3: 572 peptides, 86 chains. Longest chain 18 peptides. Score 0.494 Round 4: 586 peptides, 84 chains. Longest chain 27 peptides. Score 0.521 Round 5: 606 peptides, 84 chains. Longest chain 19 peptides. Score 0.544 Taking the results from Round 5 Chains 84, Residues 522, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19203 restraints for refining 8208 atoms. 17199 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3507 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 2: After refmac, R = 0.2330 (Rfree = 0.000) for 8037 atoms. Found 28 (38 requested) and removed 47 (19 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2664 (Rfree = 0.000) for 7957 atoms. Found 38 (38 requested) and removed 56 (19 requested) atoms. Cycle 4: After refmac, R = 0.2342 (Rfree = 0.000) for 7883 atoms. Found 18 (37 requested) and removed 35 (18 requested) atoms. Cycle 5: After refmac, R = 0.2275 (Rfree = 0.000) for 7836 atoms. Found 29 (37 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8101 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 8126 seeds are put forward Round 1: 473 peptides, 93 chains. Longest chain 12 peptides. Score 0.323 Round 2: 547 peptides, 83 chains. Longest chain 15 peptides. Score 0.480 Round 3: 582 peptides, 87 chains. Longest chain 22 peptides. Score 0.501 Round 4: 585 peptides, 84 chains. Longest chain 20 peptides. Score 0.520 Round 5: 596 peptides, 78 chains. Longest chain 21 peptides. Score 0.562 Taking the results from Round 5 Chains 79, Residues 518, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18753 restraints for refining 8208 atoms. 16665 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2829 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 72 (19 requested) atoms. Cycle 7: After refmac, R = 0.2461 (Rfree = 0.000) for 8083 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 8: After refmac, R = 0.2209 (Rfree = 0.000) for 8017 atoms. Found 22 (38 requested) and removed 46 (19 requested) atoms. Cycle 9: After refmac, R = 0.2170 (Rfree = 0.000) for 7965 atoms. Found 36 (37 requested) and removed 46 (18 requested) atoms. Cycle 10: After refmac, R = 0.1781 (Rfree = 0.000) for 7925 atoms. Found 10 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 8149 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 8162 seeds are put forward Round 1: 506 peptides, 93 chains. Longest chain 11 peptides. Score 0.370 Round 2: 574 peptides, 89 chains. Longest chain 16 peptides. Score 0.481 Round 3: 587 peptides, 87 chains. Longest chain 18 peptides. Score 0.507 Round 4: 608 peptides, 84 chains. Longest chain 17 peptides. Score 0.546 Round 5: 603 peptides, 83 chains. Longest chain 23 peptides. Score 0.545 Taking the results from Round 4 Chains 84, Residues 524, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18724 restraints for refining 8208 atoms. 16700 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2880 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 93 (19 requested) atoms. Cycle 12: After refmac, R = 0.2535 (Rfree = 0.000) for 8082 atoms. Found 38 (38 requested) and removed 65 (19 requested) atoms. Cycle 13: After refmac, R = 0.2187 (Rfree = 0.000) for 8015 atoms. Found 22 (38 requested) and removed 33 (19 requested) atoms. Cycle 14: After refmac, R = 0.2287 (Rfree = 0.000) for 7980 atoms. Found 20 (38 requested) and removed 42 (19 requested) atoms. Cycle 15: After refmac, R = 0.2369 (Rfree = 0.000) for 7950 atoms. Found 12 (37 requested) and removed 36 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 8166 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 8183 seeds are put forward Round 1: 522 peptides, 93 chains. Longest chain 15 peptides. Score 0.392 Round 2: 557 peptides, 87 chains. Longest chain 17 peptides. Score 0.470 Round 3: 547 peptides, 82 chains. Longest chain 17 peptides. Score 0.485 Round 4: 541 peptides, 75 chains. Longest chain 27 peptides. Score 0.515 Round 5: 550 peptides, 76 chains. Longest chain 19 peptides. Score 0.520 Taking the results from Round 5 Chains 77, Residues 474, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19009 restraints for refining 8207 atoms. 17162 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2890 (Rfree = 0.000) for 8207 atoms. Found 38 (38 requested) and removed 55 (19 requested) atoms. Cycle 17: After refmac, R = 0.2806 (Rfree = 0.000) for 8128 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 18: After refmac, R = 0.2418 (Rfree = 0.000) for 8078 atoms. Found 28 (38 requested) and removed 34 (19 requested) atoms. Cycle 19: After refmac, R = 0.2496 (Rfree = 0.000) for 8037 atoms. Found 23 (38 requested) and removed 37 (19 requested) atoms. Cycle 20: After refmac, R = 0.1808 (Rfree = 0.000) for 8015 atoms. Found 8 (38 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 8231 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 8252 seeds are put forward Round 1: 463 peptides, 93 chains. Longest chain 14 peptides. Score 0.308 Round 2: 542 peptides, 82 chains. Longest chain 16 peptides. Score 0.479 Round 3: 532 peptides, 83 chains. Longest chain 16 peptides. Score 0.461 Round 4: 528 peptides, 77 chains. Longest chain 17 peptides. Score 0.489 Round 5: 566 peptides, 80 chains. Longest chain 22 peptides. Score 0.518 Taking the results from Round 5 Chains 80, Residues 486, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19225 restraints for refining 8208 atoms. 17361 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2739 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 22: After refmac, R = 0.2493 (Rfree = 0.000) for 8121 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 23: After refmac, R = 0.1998 (Rfree = 0.000) for 8054 atoms. Found 28 (38 requested) and removed 29 (19 requested) atoms. Cycle 24: After refmac, R = 0.1808 (Rfree = 0.000) for 8020 atoms. Found 11 (38 requested) and removed 30 (19 requested) atoms. Cycle 25: After refmac, R = 0.1667 (Rfree = 0.000) for 7986 atoms. Found 11 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8188 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8204 seeds are put forward Round 1: 423 peptides, 87 chains. Longest chain 10 peptides. Score 0.286 Round 2: 495 peptides, 81 chains. Longest chain 15 peptides. Score 0.425 Round 3: 505 peptides, 79 chains. Longest chain 15 peptides. Score 0.449 Round 4: 531 peptides, 78 chains. Longest chain 18 peptides. Score 0.487 Round 5: 540 peptides, 76 chains. Longest chain 30 peptides. Score 0.509 Taking the results from Round 5 Chains 78, Residues 464, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18884 restraints for refining 8206 atoms. 17060 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2435 (Rfree = 0.000) for 8206 atoms. Found 38 (38 requested) and removed 56 (19 requested) atoms. Cycle 27: After refmac, R = 0.2477 (Rfree = 0.000) for 8132 atoms. Found 38 (38 requested) and removed 60 (19 requested) atoms. Cycle 28: After refmac, R = 0.2313 (Rfree = 0.000) for 8073 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 29: After refmac, R = 0.2318 (Rfree = 0.000) for 8034 atoms. Found 38 (38 requested) and removed 49 (19 requested) atoms. Cycle 30: After refmac, R = 0.1834 (Rfree = 0.000) for 7994 atoms. Found 23 (38 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 8207 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 8223 seeds are put forward Round 1: 381 peptides, 79 chains. Longest chain 10 peptides. Score 0.273 Round 2: 463 peptides, 78 chains. Longest chain 12 peptides. Score 0.399 Round 3: 460 peptides, 73 chains. Longest chain 15 peptides. Score 0.425 Round 4: 468 peptides, 79 chains. Longest chain 14 peptides. Score 0.400 Round 5: 451 peptides, 69 chains. Longest chain 15 peptides. Score 0.436 Taking the results from Round 5 Chains 70, Residues 382, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19489 restraints for refining 8208 atoms. 17996 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2561 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 49 (19 requested) atoms. Cycle 32: After refmac, R = 0.2521 (Rfree = 0.000) for 8134 atoms. Found 38 (38 requested) and removed 54 (19 requested) atoms. Cycle 33: After refmac, R = 0.2569 (Rfree = 0.000) for 8084 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 34: After refmac, R = 0.2454 (Rfree = 0.000) for 8052 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 35: After refmac, R = 0.1901 (Rfree = 0.000) for 8016 atoms. Found 28 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8199 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8215 seeds are put forward Round 1: 352 peptides, 74 chains. Longest chain 14 peptides. Score 0.261 Round 2: 408 peptides, 74 chains. Longest chain 11 peptides. Score 0.346 Round 3: 419 peptides, 72 chains. Longest chain 11 peptides. Score 0.374 Round 4: 436 peptides, 74 chains. Longest chain 13 peptides. Score 0.386 Round 5: 425 peptides, 72 chains. Longest chain 15 peptides. Score 0.383 Taking the results from Round 4 Chains 74, Residues 362, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19486 restraints for refining 8160 atoms. 18112 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2467 (Rfree = 0.000) for 8160 atoms. Found 38 (38 requested) and removed 205 (19 requested) atoms. Cycle 37: After refmac, R = 0.2505 (Rfree = 0.000) for 7951 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 38: After refmac, R = 0.2362 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 53 (18 requested) atoms. Cycle 39: After refmac, R = 0.2152 (Rfree = 0.000) for 7860 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 40: After refmac, R = 0.2072 (Rfree = 0.000) for 7841 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 8037 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8050 seeds are put forward Round 1: 360 peptides, 75 chains. Longest chain 13 peptides. Score 0.267 Round 2: 416 peptides, 78 chains. Longest chain 9 peptides. Score 0.333 Round 3: 441 peptides, 79 chains. Longest chain 15 peptides. Score 0.362 Round 4: 447 peptides, 74 chains. Longest chain 19 peptides. Score 0.401 Round 5: 431 peptides, 73 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 4 Chains 74, Residues 373, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18833 restraints for refining 8045 atoms. 17415 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2540 (Rfree = 0.000) for 8045 atoms. Found 38 (38 requested) and removed 56 (19 requested) atoms. Cycle 42: After refmac, R = 0.2258 (Rfree = 0.000) for 7972 atoms. Found 38 (38 requested) and removed 42 (19 requested) atoms. Cycle 43: After refmac, R = 0.2345 (Rfree = 0.000) for 7927 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 44: After refmac, R = 0.2241 (Rfree = 0.000) for 7898 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 45: After refmac, R = 0.1755 (Rfree = 0.000) for 7868 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 8040 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8053 seeds are put forward Round 1: 325 peptides, 69 chains. Longest chain 12 peptides. Score 0.251 Round 2: 367 peptides, 69 chains. Longest chain 12 peptides. Score 0.317 Round 3: 392 peptides, 75 chains. Longest chain 11 peptides. Score 0.316 Round 4: 407 peptides, 73 chains. Longest chain 12 peptides. Score 0.351 Round 5: 413 peptides, 70 chains. Longest chain 16 peptides. Score 0.378 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 343, 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 2hx1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10515 reflections ( 99.59 % complete ) and 18617 restraints for refining 7890 atoms. 17315 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2320 (Rfree = 0.000) for 7890 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2321 (Rfree = 0.000) for 7828 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2247 (Rfree = 0.000) for 7782 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1786 (Rfree = 0.000) for 7738 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... TimeTaking 74.68