Sun 23 Dec 22:23:10 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 1zy9-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.2-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/1zy9-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.2-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 22:23:20 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/1zy9-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.2-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 641 and 0 Target number of residues in the AU: 641 Target solvent content: 0.5985 Checking the provided sequence file Detected sequence length: 564 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 564 Adjusted target solvent content: 0.65 Input MTZ file: 1zy9-3.2-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: 20 Cell parameters: 121.755 160.844 88.238 90.000 90.000 90.000 Input sequence file: 1zy9-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4512 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 Loops will be built when appropriate and at the last cycle Resolution range: 97.078 3.200 Wilson plot Bfac: 51.77 14133 reflections ( 96.37 % complete ) and 0 restraints for refining 4982 atoms. Observations/parameters ratio is 0.71 ------------------------------------------------------ Starting model: R = 0.3038 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2843 (Rfree = 0.000) for 4982 atoms. Found 44 (44 requested) and removed 36 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 2.50 Search for helices and strands: 0 residues in 0 chains, 5077 seeds are put forward Round 1: 319 peptides, 54 chains. Longest chain 12 peptides. Score 0.388 Round 2: 382 peptides, 52 chains. Longest chain 18 peptides. Score 0.514 Round 3: 416 peptides, 46 chains. Longest chain 26 peptides. Score 0.607 Round 4: 412 peptides, 45 chains. Longest chain 24 peptides. Score 0.608 Round 5: 418 peptides, 39 chains. Longest chain 46 peptides. Score 0.653 Taking the results from Round 5 Chains 40, Residues 379, Estimated correctness of the model 54.6 % 6 chains (117 residues) have been docked in sequence ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 7494 restraints for refining 4119 atoms. 5551 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2805 (Rfree = 0.000) for 4119 atoms. Found 36 (36 requested) and removed 29 (18 requested) atoms. Cycle 2: After refmac, R = 0.2692 (Rfree = 0.000) for 4053 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. Cycle 3: After refmac, R = 0.2599 (Rfree = 0.000) for 4030 atoms. Found 36 (36 requested) and removed 22 (18 requested) atoms. Cycle 4: After refmac, R = 0.2566 (Rfree = 0.000) for 4026 atoms. Found 33 (36 requested) and removed 21 (18 requested) atoms. Cycle 5: After refmac, R = 0.2545 (Rfree = 0.000) for 4025 atoms. Found 36 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 2.44 Search for helices and strands: 0 residues in 0 chains, 4189 seeds are put forward Round 1: 400 peptides, 40 chains. Longest chain 37 peptides. Score 0.623 Round 2: 442 peptides, 35 chains. Longest chain 45 peptides. Score 0.704 Round 3: 434 peptides, 37 chains. Longest chain 41 peptides. Score 0.684 Round 4: 443 peptides, 36 chains. Longest chain 49 peptides. Score 0.700 Round 5: 437 peptides, 33 chains. Longest chain 50 peptides. Score 0.710 Taking the results from Round 5 Chains 35, Residues 404, Estimated correctness of the model 67.3 % 5 chains (129 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 154 A and 162 A 33 chains (407 residues) following loop building 4 chains (136 residues) in sequence following loop building ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 7275 restraints for refining 4119 atoms. 5293 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2867 (Rfree = 0.000) for 4119 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. Cycle 7: After refmac, R = 0.2689 (Rfree = 0.000) for 4081 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. Cycle 8: After refmac, R = 0.2573 (Rfree = 0.000) for 4071 atoms. Found 35 (35 requested) and removed 23 (18 requested) atoms. Cycle 9: After refmac, R = 0.2475 (Rfree = 0.000) for 4064 atoms. Found 33 (34 requested) and removed 26 (18 requested) atoms. Cycle 10: After refmac, R = 0.2403 (Rfree = 0.000) for 4056 atoms. Found 24 (33 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 2.47 Search for helices and strands: 0 residues in 0 chains, 4185 seeds are put forward Round 1: 429 peptides, 42 chains. Longest chain 40 peptides. Score 0.649 Round 2: 437 peptides, 31 chains. Longest chain 51 peptides. Score 0.721 Round 3: 438 peptides, 39 chains. Longest chain 47 peptides. Score 0.677 Round 4: 453 peptides, 35 chains. Longest chain 53 peptides. Score 0.716 Round 5: 448 peptides, 34 chains. Longest chain 44 peptides. Score 0.716 Taking the results from Round 2 Chains 34, Residues 406, Estimated correctness of the model 69.5 % 9 chains (205 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 381 A and 387 A 32 chains (410 residues) following loop building 8 chains (210 residues) in sequence following loop building ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 6469 restraints for refining 4119 atoms. 3970 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2798 (Rfree = 0.000) for 4119 atoms. Found 32 (32 requested) and removed 40 (18 requested) atoms. Cycle 12: After refmac, R = 0.2575 (Rfree = 0.000) for 4078 atoms. Found 30 (32 requested) and removed 28 (18 requested) atoms. Cycle 13: After refmac, R = 0.2464 (Rfree = 0.000) for 4052 atoms. Found 22 (31 requested) and removed 27 (18 requested) atoms. Cycle 14: After refmac, R = 0.2405 (Rfree = 0.000) for 4033 atoms. Found 19 (30 requested) and removed 21 (18 requested) atoms. Cycle 15: After refmac, R = 0.2345 (Rfree = 0.000) for 4023 atoms. Found 14 (30 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 2.43 Search for helices and strands: 0 residues in 0 chains, 4109 seeds are put forward Round 1: 419 peptides, 34 chains. Longest chain 47 peptides. Score 0.684 Round 2: 452 peptides, 36 chains. Longest chain 50 peptides. Score 0.710 Round 3: 441 peptides, 35 chains. Longest chain 47 peptides. Score 0.703 Round 4: 451 peptides, 36 chains. Longest chain 33 peptides. Score 0.709 Round 5: 448 peptides, 30 chains. Longest chain 47 peptides. Score 0.737 Taking the results from Round 5 Chains 36, Residues 418, Estimated correctness of the model 72.6 % 9 chains (190 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 107 A 34 chains (418 residues) following loop building 8 chains (195 residues) in sequence following loop building ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 6449 restraints for refining 4118 atoms. 4007 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2790 (Rfree = 0.000) for 4118 atoms. Found 29 (29 requested) and removed 39 (18 requested) atoms. Cycle 17: After refmac, R = 0.2685 (Rfree = 0.000) for 4077 atoms. Found 28 (28 requested) and removed 29 (18 requested) atoms. Cycle 18: After refmac, R = 0.2651 (Rfree = 0.000) for 4057 atoms. Found 27 (27 requested) and removed 27 (18 requested) atoms. Cycle 19: After refmac, R = 0.2630 (Rfree = 0.000) for 4041 atoms. Found 27 (27 requested) and removed 24 (18 requested) atoms. Cycle 20: After refmac, R = 0.2530 (Rfree = 0.000) for 4038 atoms. Found 25 (26 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 2.49 Search for helices and strands: 0 residues in 0 chains, 4168 seeds are put forward Round 1: 426 peptides, 44 chains. Longest chain 34 peptides. Score 0.633 Round 2: 447 peptides, 33 chains. Longest chain 33 peptides. Score 0.721 Round 3: 450 peptides, 35 chains. Longest chain 74 peptides. Score 0.713 Round 4: 434 peptides, 32 chains. Longest chain 56 peptides. Score 0.712 Round 5: 421 peptides, 36 chains. Longest chain 54 peptides. Score 0.675 Taking the results from Round 2 Chains 35, Residues 414, Estimated correctness of the model 69.5 % 6 chains (130 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 197 A and 207 A 32 chains (419 residues) following loop building 5 chains (139 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 14133 reflections ( 96.37 % complete ) and 7006 restraints for refining 4119 atoms. 4707 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2680 (Rfree = 0.000) for 4119 atoms. Found 25 (25 requested) and removed 36 (18 requested) atoms. Cycle 22: After refmac, R = 0.2576 (Rfree = 0.000) for 4087 atoms. Found 24 (24 requested) and removed 28 (18 requested) atoms. Cycle 23: After refmac, R = 0.2526 (Rfree = 0.000) for 4072 atoms. Found 21 (24 requested) and removed 25 (18 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 24: After refmac, R = 0.2444 (Rfree = 0.000) for 4065 atoms. Found 15 (23 requested) and removed 19 (18 requested) atoms. Cycle 25: After refmac, R = 0.2391 (Rfree = 0.000) for 4054 atoms. Found 9 (22 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 2.45 Search for helices and strands: 0 residues in 0 chains, 4138 seeds are put forward Round 1: 420 peptides, 35 chains. Longest chain 36 peptides. Score 0.679 Round 2: 449 peptides, 35 chains. Longest chain 36 peptides. Score 0.712 Round 3: 444 peptides, 35 chains. Longest chain 41 peptides. Score 0.707 Round 4: 440 peptides, 34 chains. Longest chain 64 peptides. Score 0.708 Round 5: 439 peptides, 34 chains. Longest chain 35 peptides. Score 0.707 Taking the results from Round 2 Chains 37, Residues 414, Estimated correctness of the model 67.7 % 6 chains (142 residues) have been docked in sequence Building loops using Loopy2018 37 chains (414 residues) following loop building 6 chains (142 residues) in sequence following loop building ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 7154 restraints for refining 4118 atoms. 4899 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2531 (Rfree = 0.000) for 4118 atoms. Found 22 (22 requested) and removed 36 (18 requested) atoms. Cycle 27: After refmac, R = 0.2375 (Rfree = 0.000) for 4090 atoms. Found 21 (21 requested) and removed 26 (18 requested) atoms. Cycle 28: After refmac, R = 0.2296 (Rfree = 0.000) for 4075 atoms. Found 19 (20 requested) and removed 19 (18 requested) atoms. Cycle 29: After refmac, R = 0.2238 (Rfree = 0.000) for 4065 atoms. Found 18 (19 requested) and removed 19 (18 requested) atoms. Cycle 30: After refmac, R = 0.2177 (Rfree = 0.000) for 4054 atoms. Found 19 (19 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 2.45 Search for helices and strands: 0 residues in 0 chains, 4147 seeds are put forward Round 1: 422 peptides, 39 chains. Longest chain 51 peptides. Score 0.658 Round 2: 445 peptides, 36 chains. Longest chain 42 peptides. Score 0.702 Round 3: 454 peptides, 38 chains. Longest chain 51 peptides. Score 0.701 Round 4: 450 peptides, 37 chains. Longest chain 58 peptides. Score 0.702 Round 5: 463 peptides, 36 chains. Longest chain 46 peptides. Score 0.722 Taking the results from Round 5 Chains 40, Residues 427, Estimated correctness of the model 69.7 % 9 chains (177 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 246 A and 250 A 39 chains (426 residues) following loop building 8 chains (180 residues) in sequence following loop building ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 6721 restraints for refining 4117 atoms. 4302 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2715 (Rfree = 0.000) for 4117 atoms. Found 18 (18 requested) and removed 40 (18 requested) atoms. Cycle 32: After refmac, R = 0.2554 (Rfree = 0.000) for 4081 atoms. Found 18 (18 requested) and removed 24 (18 requested) atoms. Cycle 33: After refmac, R = 0.2523 (Rfree = 0.000) for 4064 atoms. Found 18 (18 requested) and removed 19 (18 requested) atoms. Cycle 34: After refmac, R = 0.2479 (Rfree = 0.000) for 4058 atoms. Found 18 (18 requested) and removed 21 (18 requested) atoms. Cycle 35: After refmac, R = 0.2440 (Rfree = 0.000) for 4054 atoms. Found 15 (18 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 2.49 Search for helices and strands: 0 residues in 0 chains, 4154 seeds are put forward Round 1: 416 peptides, 43 chains. Longest chain 36 peptides. Score 0.626 Round 2: 433 peptides, 30 chains. Longest chain 51 peptides. Score 0.722 Round 3: 418 peptides, 41 chains. Longest chain 28 peptides. Score 0.641 Round 4: 417 peptides, 39 chains. Longest chain 36 peptides. Score 0.652 Round 5: 430 peptides, 37 chains. Longest chain 32 peptides. Score 0.679 Taking the results from Round 2 Chains 33, Residues 403, Estimated correctness of the model 69.7 % 7 chains (199 residues) have been docked in sequence Building loops using Loopy2018 33 chains (403 residues) following loop building 7 chains (199 residues) in sequence following loop building ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 6636 restraints for refining 4118 atoms. 4138 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2742 (Rfree = 0.000) for 4118 atoms. Found 18 (18 requested) and removed 48 (18 requested) atoms. Cycle 37: After refmac, R = 0.2585 (Rfree = 0.000) for 4063 atoms. Found 18 (18 requested) and removed 26 (18 requested) atoms. Cycle 38: After refmac, R = 0.2517 (Rfree = 0.000) for 4043 atoms. Found 18 (18 requested) and removed 21 (18 requested) atoms. Cycle 39: After refmac, R = 0.2464 (Rfree = 0.000) for 4037 atoms. Found 15 (18 requested) and removed 18 (18 requested) atoms. Cycle 40: After refmac, R = 0.2420 (Rfree = 0.000) for 4027 atoms. Found 18 (18 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 2.47 Search for helices and strands: 0 residues in 0 chains, 4121 seeds are put forward Round 1: 409 peptides, 41 chains. Longest chain 39 peptides. Score 0.629 Round 2: 423 peptides, 35 chains. Longest chain 48 peptides. Score 0.683 Round 3: 430 peptides, 37 chains. Longest chain 33 peptides. Score 0.679 Round 4: 434 peptides, 37 chains. Longest chain 29 peptides. Score 0.684 Round 5: 423 peptides, 33 chains. Longest chain 36 peptides. Score 0.694 Taking the results from Round 5 Chains 36, Residues 390, Estimated correctness of the model 63.9 % 8 chains (161 residues) have been docked in sequence ------------------------------------------------------ 14133 reflections ( 96.37 % complete ) and 7091 restraints for refining 4119 atoms. 4851 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2708 (Rfree = 0.000) for 4119 atoms. Found 18 (18 requested) and removed 37 (18 requested) atoms. Cycle 42: After refmac, R = 0.2562 (Rfree = 0.000) for 4084 atoms. Found 18 (18 requested) and removed 27 (18 requested) atoms. Cycle 43: After refmac, R = 0.2492 (Rfree = 0.000) for 4067 atoms. Found 18 (18 requested) and removed 19 (18 requested) atoms. Cycle 44: After refmac, R = 0.2440 (Rfree = 0.000) for 4056 atoms. Found 18 (18 requested) and removed 20 (18 requested) atoms. Cycle 45: After refmac, R = 0.2397 (Rfree = 0.000) for 4049 atoms. Found 18 (18 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 2.50 Search for helices and strands: 0 residues in 0 chains, 4157 seeds are put forward Round 1: 407 peptides, 40 chains. Longest chain 30 peptides. Score 0.633 Round 2: 431 peptides, 37 chains. Longest chain 42 peptides. Score 0.681 Round 3: 426 peptides, 40 chains. Longest chain 27 peptides. Score 0.657 Round 4: 425 peptides, 38 chains. Longest chain 33 peptides. Score 0.668 Round 5: 424 peptides, 32 chains. Longest chain 41 peptides. Score 0.701 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 392, Estimated correctness of the model 65.4 % 6 chains (153 residues) have been docked in sequence Sequence coverage is 38 % Consider running further cycles of model building using 1zy9-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (392 residues) following loop building 6 chains (153 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14133 reflections ( 96.37 % complete ) and 7102 restraints for refining 4119 atoms. 4878 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2716 (Rfree = 0.000) for 4119 atoms. Found 0 (18 requested) and removed 12 (18 requested) atoms. Cycle 47: After refmac, R = 0.2667 (Rfree = 0.000) for 4089 atoms. Found 0 (18 requested) and removed 10 (18 requested) atoms. Cycle 48: After refmac, R = 0.2653 (Rfree = 0.000) for 4071 atoms. Found 0 (18 requested) and removed 5 (18 requested) atoms. Cycle 49: After refmac, R = 0.2598 (Rfree = 0.000) for 4058 atoms. TimeTaking 70.82