Sun 23 Dec 22:22:43 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 2hr2-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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/2hr2-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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 22:22:53 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/2hr2-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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 865 and 0 Target number of residues in the AU: 865 Target solvent content: 0.6732 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-4.0-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.80 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: 88.085 4.000 Wilson plot Bfac: 95.09 Failed to save intermediate PDB 12411 reflections ( 97.90 % complete ) and 0 restraints for refining 8400 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3639 (Rfree = 0.000) for 8400 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.22 Search for helices and strands: 0 residues in 0 chains, 8713 seeds are put forward NCS extension: 0 residues added, 8713 seeds are put forward Round 1: 365 peptides, 52 chains. Longest chain 19 peptides. Score 0.393 Round 2: 447 peptides, 45 chains. Longest chain 23 peptides. Score 0.520 Round 3: 485 peptides, 38 chains. Longest chain 28 peptides. Score 0.589 Round 4: 473 peptides, 39 chains. Longest chain 27 peptides. Score 0.574 Round 5: 484 peptides, 40 chains. Longest chain 28 peptides. Score 0.579 Taking the results from Round 3 Chains 42, Residues 447, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15114 restraints for refining 6696 atoms. 13291 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2611 (Rfree = 0.000) for 6696 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 2: After refmac, R = 0.2472 (Rfree = 0.000) for 6541 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 3: After refmac, R = 0.2340 (Rfree = 0.000) for 6489 atoms. Found 27 (31 requested) and removed 37 (15 requested) atoms. Cycle 4: After refmac, R = 0.2038 (Rfree = 0.000) for 6435 atoms. Found 6 (30 requested) and removed 32 (15 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2013 (Rfree = 0.000) for 6380 atoms. Found 11 (30 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.86 3.19 Search for helices and strands: 0 residues in 0 chains, 6773 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6789 seeds are put forward Round 1: 436 peptides, 58 chains. Longest chain 21 peptides. Score 0.443 Round 2: 470 peptides, 47 chains. Longest chain 24 peptides. Score 0.533 Round 3: 480 peptides, 46 chains. Longest chain 23 peptides. Score 0.548 Round 4: 472 peptides, 45 chains. Longest chain 27 peptides. Score 0.545 Round 5: 486 peptides, 46 chains. Longest chain 36 peptides. Score 0.553 Taking the results from Round 5 Chains 46, Residues 440, Estimated correctness of the model 0.0 % 1 chains (35 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 14835 restraints for refining 6757 atoms. 12986 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2528 (Rfree = 0.000) for 6757 atoms. Found 32 (32 requested) and removed 61 (16 requested) atoms. Cycle 7: After refmac, R = 0.2301 (Rfree = 0.000) for 6660 atoms. Found 31 (31 requested) and removed 62 (15 requested) atoms. Cycle 8: After refmac, R = 0.2250 (Rfree = 0.000) for 6565 atoms. Found 31 (31 requested) and removed 61 (15 requested) atoms. Cycle 9: After refmac, R = 0.2168 (Rfree = 0.000) for 6483 atoms. Found 31 (31 requested) and removed 51 (15 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1921 (Rfree = 0.000) for 6441 atoms. Found 12 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.86 3.19 Search for helices and strands: 0 residues in 0 chains, 6844 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6868 seeds are put forward Round 1: 444 peptides, 62 chains. Longest chain 19 peptides. Score 0.431 Round 2: 480 peptides, 53 chains. Longest chain 26 peptides. Score 0.514 Round 3: 481 peptides, 50 chains. Longest chain 42 peptides. Score 0.530 Round 4: 472 peptides, 46 chains. Longest chain 27 peptides. Score 0.540 Round 5: 486 peptides, 44 chains. Longest chain 25 peptides. Score 0.563 Taking the results from Round 5 Chains 51, Residues 442, Estimated correctness of the model 0.0 % 8 chains (80 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 14550 restraints for refining 6891 atoms. 12520 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2542 (Rfree = 0.000) for 6891 atoms. Found 32 (32 requested) and removed 52 (16 requested) atoms. Cycle 12: After refmac, R = 0.2399 (Rfree = 0.000) for 6777 atoms. Found 32 (32 requested) and removed 71 (16 requested) atoms. Cycle 13: After refmac, R = 0.2233 (Rfree = 0.000) for 6690 atoms. Found 32 (32 requested) and removed 53 (16 requested) atoms. Cycle 14: After refmac, R = 0.2251 (Rfree = 0.000) for 6633 atoms. Found 31 (31 requested) and removed 58 (15 requested) atoms. Cycle 15: After refmac, R = 0.2169 (Rfree = 0.000) for 6586 atoms. Found 31 (31 requested) and removed 53 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.17 Search for helices and strands: 0 residues in 0 chains, 6936 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 6966 seeds are put forward Round 1: 439 peptides, 65 chains. Longest chain 19 peptides. Score 0.410 Round 2: 475 peptides, 54 chains. Longest chain 22 peptides. Score 0.504 Round 3: 502 peptides, 55 chains. Longest chain 33 peptides. Score 0.527 Round 4: 496 peptides, 55 chains. Longest chain 22 peptides. Score 0.521 Round 5: 475 peptides, 53 chains. Longest chain 23 peptides. Score 0.509 Taking the results from Round 3 Chains 58, Residues 447, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 14570 restraints for refining 6838 atoms. 12688 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2469 (Rfree = 0.000) for 6838 atoms. Found 32 (32 requested) and removed 103 (16 requested) atoms. Cycle 17: After refmac, R = 0.2268 (Rfree = 0.000) for 6704 atoms. Found 32 (32 requested) and removed 56 (16 requested) atoms. Cycle 18: After refmac, R = 0.2250 (Rfree = 0.000) for 6649 atoms. Found 24 (31 requested) and removed 60 (15 requested) atoms. Cycle 19: After refmac, R = 0.2149 (Rfree = 0.000) for 6592 atoms. Found 31 (31 requested) and removed 57 (15 requested) atoms. Cycle 20: After refmac, R = 0.2127 (Rfree = 0.000) for 6538 atoms. Found 26 (31 requested) and removed 38 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.16 Search for helices and strands: 0 residues in 0 chains, 6956 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6979 seeds are put forward Round 1: 444 peptides, 68 chains. Longest chain 23 peptides. Score 0.400 Round 2: 471 peptides, 57 chains. Longest chain 26 peptides. Score 0.486 Round 3: 464 peptides, 60 chains. Longest chain 23 peptides. Score 0.463 Round 4: 441 peptides, 49 chains. Longest chain 33 peptides. Score 0.494 Round 5: 455 peptides, 54 chains. Longest chain 23 peptides. Score 0.484 Taking the results from Round 4 Chains 52, Residues 392, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12411 reflections ( 97.90 % complete ) and 15101 restraints for refining 6892 atoms. 13440 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2410 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 93 (16 requested) atoms. Cycle 22: After refmac, R = 0.2376 (Rfree = 0.000) for 6783 atoms. Found 29 (32 requested) and removed 70 (16 requested) atoms. Cycle 23: After refmac, R = 0.2310 (Rfree = 0.000) for 6703 atoms. Found 32 (32 requested) and removed 63 (16 requested) atoms. Cycle 24: After refmac, R = 0.2260 (Rfree = 0.000) for 6636 atoms. Found 30 (31 requested) and removed 47 (15 requested) atoms. Cycle 25: After refmac, R = 0.1954 (Rfree = 0.000) for 6591 atoms. Found 10 (31 requested) and removed 38 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.16 Search for helices and strands: 0 residues in 0 chains, 6926 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 6962 seeds are put forward Round 1: 418 peptides, 72 chains. Longest chain 12 peptides. Score 0.347 Round 2: 452 peptides, 57 chains. Longest chain 23 peptides. Score 0.465 Round 3: 460 peptides, 59 chains. Longest chain 23 peptides. Score 0.464 Round 4: 475 peptides, 66 chains. Longest chain 18 peptides. Score 0.445 Round 5: 469 peptides, 60 chains. Longest chain 21 peptides. Score 0.469 Taking the results from Round 5 Chains 61, Residues 409, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15252 restraints for refining 6891 atoms. 13574 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2651 (Rfree = 0.000) for 6891 atoms. Found 32 (32 requested) and removed 54 (16 requested) atoms. Cycle 27: After refmac, R = 0.2542 (Rfree = 0.000) for 6801 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. Cycle 28: After refmac, R = 0.2379 (Rfree = 0.000) for 6740 atoms. Found 26 (32 requested) and removed 46 (16 requested) atoms. Cycle 29: After refmac, R = 0.2108 (Rfree = 0.000) for 6684 atoms. Found 16 (31 requested) and removed 29 (15 requested) atoms. Cycle 30: After refmac, R = 0.2068 (Rfree = 0.000) for 6653 atoms. Found 10 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.16 Search for helices and strands: 0 residues in 0 chains, 6982 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 7006 seeds are put forward Round 1: 397 peptides, 67 chains. Longest chain 12 peptides. Score 0.348 Round 2: 430 peptides, 60 chains. Longest chain 17 peptides. Score 0.425 Round 3: 438 peptides, 57 chains. Longest chain 22 peptides. Score 0.450 Round 4: 431 peptides, 56 chains. Longest chain 24 peptides. Score 0.448 Round 5: 436 peptides, 56 chains. Longest chain 17 peptides. Score 0.453 Taking the results from Round 5 Chains 56, Residues 380, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15600 restraints for refining 6891 atoms. 14110 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2544 (Rfree = 0.000) for 6891 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. Cycle 32: After refmac, R = 0.2392 (Rfree = 0.000) for 6818 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 33: After refmac, R = 0.2289 (Rfree = 0.000) for 6765 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. Cycle 34: After refmac, R = 0.2220 (Rfree = 0.000) for 6711 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 35: After refmac, R = 0.1879 (Rfree = 0.000) for 6666 atoms. Found 7 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.15 Search for helices and strands: 0 residues in 0 chains, 6983 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 6996 seeds are put forward Round 1: 372 peptides, 70 chains. Longest chain 14 peptides. Score 0.299 Round 2: 418 peptides, 70 chains. Longest chain 14 peptides. Score 0.358 Round 3: 433 peptides, 72 chains. Longest chain 13 peptides. Score 0.365 Round 4: 432 peptides, 68 chains. Longest chain 14 peptides. Score 0.386 Round 5: 424 peptides, 65 chains. Longest chain 16 peptides. Score 0.392 Taking the results from Round 5 Chains 65, Residues 359, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12411 reflections ( 97.90 % complete ) and 15724 restraints for refining 6893 atoms. 14330 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2590 (Rfree = 0.000) for 6893 atoms. Found 32 (32 requested) and removed 85 (16 requested) atoms. Cycle 37: After refmac, R = 0.2483 (Rfree = 0.000) for 6786 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 38: After refmac, R = 0.2434 (Rfree = 0.000) for 6747 atoms. Found 32 (32 requested) and removed 74 (16 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2170 (Rfree = 0.000) for 6672 atoms. Found 9 (31 requested) and removed 39 (15 requested) atoms. Cycle 40: After refmac, R = 0.2121 (Rfree = 0.000) for 6621 atoms. Found 15 (31 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.17 Search for helices and strands: 0 residues in 0 chains, 6946 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6969 seeds are put forward Round 1: 348 peptides, 66 chains. Longest chain 12 peptides. Score 0.291 Round 2: 403 peptides, 67 chains. Longest chain 20 peptides. Score 0.356 Round 3: 408 peptides, 61 chains. Longest chain 22 peptides. Score 0.395 Round 4: 401 peptides, 64 chains. Longest chain 23 peptides. Score 0.370 Round 5: 398 peptides, 62 chains. Longest chain 18 peptides. Score 0.377 Taking the results from Round 3 Chains 63, Residues 347, Estimated correctness of the model 0.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15115 restraints for refining 6852 atoms. 13652 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2525 (Rfree = 0.000) for 6852 atoms. Found 32 (32 requested) and removed 56 (16 requested) atoms. Cycle 42: After refmac, R = 0.2334 (Rfree = 0.000) for 6798 atoms. Found 32 (32 requested) and removed 54 (16 requested) atoms. Cycle 43: After refmac, R = 0.2234 (Rfree = 0.000) for 6753 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 44: After refmac, R = 0.2252 (Rfree = 0.000) for 6732 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 45: After refmac, R = 0.2223 (Rfree = 0.000) for 6715 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.17 Search for helices and strands: 0 residues in 0 chains, 7032 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 7056 seeds are put forward Round 1: 347 peptides, 66 chains. Longest chain 10 peptides. Score 0.289 Round 2: 395 peptides, 66 chains. Longest chain 13 peptides. Score 0.351 Round 3: 391 peptides, 63 chains. Longest chain 14 peptides. Score 0.363 Round 4: 400 peptides, 59 chains. Longest chain 19 peptides. Score 0.396 Round 5: 367 peptides, 58 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 341, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2hr2-4_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (341 residues) following loop building 4 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12411 reflections ( 97.90 % complete ) and 15678 restraints for refining 6890 atoms. 14282 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2478 (Rfree = 0.000) for 6890 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2415 (Rfree = 0.000) for 6840 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2304 (Rfree = 0.000) for 6787 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2278 (Rfree = 0.000) for 6741 atoms. TimeTaking 85.52