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 2hq7-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-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/2hq7-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-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 22:23:20 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/2hq7-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-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 257 and 0 Target number of residues in the AU: 257 Target solvent content: 0.5089 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-2.0-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.50 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 1 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: 89.671 2.000 Wilson plot Bfac: 25.26 19227 reflections ( 99.63 % complete ) and 0 restraints for refining 2603 atoms. Observations/parameters ratio is 1.85 ------------------------------------------------------ Starting model: R = 0.3124 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2621 (Rfree = 0.000) for 2603 atoms. Found 69 (89 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.14 2.32 NCS extension: 0 residues added, 2628 seeds are put forward Round 1: 209 peptides, 16 chains. Longest chain 22 peptides. Score 0.817 Round 2: 230 peptides, 12 chains. Longest chain 57 peptides. Score 0.886 Round 3: 235 peptides, 12 chains. Longest chain 43 peptides. Score 0.893 Round 4: 255 peptides, 6 chains. Longest chain 92 peptides. Score 0.946 Round 5: 251 peptides, 9 chains. Longest chain 85 peptides. Score 0.927 Taking the results from Round 4 Chains 6, Residues 249, Estimated correctness of the model 99.7 % 4 chains (233 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A Built loop between residues 73 B and 80 B 4 chains (257 residues) following loop building 2 chains (241 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2565 restraints for refining 2390 atoms. 508 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2745 (Rfree = 0.000) for 2390 atoms. Found 52 (81 requested) and removed 45 (40 requested) atoms. Cycle 2: After refmac, R = 0.2505 (Rfree = 0.000) for 2382 atoms. Found 58 (80 requested) and removed 41 (41 requested) atoms. Cycle 3: After refmac, R = 0.2396 (Rfree = 0.000) for 2388 atoms. Found 64 (79 requested) and removed 36 (41 requested) atoms. Cycle 4: After refmac, R = 0.2312 (Rfree = 0.000) for 2410 atoms. Found 50 (77 requested) and removed 37 (41 requested) atoms. Cycle 5: After refmac, R = 0.2243 (Rfree = 0.000) for 2415 atoms. Found 41 (75 requested) and removed 25 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.08 2.25 NCS extension: 1 residues added (2 deleted due to clashes), 2437 seeds are put forward Round 1: 255 peptides, 7 chains. Longest chain 76 peptides. Score 0.941 Round 2: 260 peptides, 6 chains. Longest chain 84 peptides. Score 0.949 Round 3: 260 peptides, 6 chains. Longest chain 76 peptides. Score 0.949 Round 4: 253 peptides, 8 chains. Longest chain 76 peptides. Score 0.934 Round 5: 256 peptides, 5 chains. Longest chain 95 peptides. Score 0.951 Taking the results from Round 5 Chains 5, Residues 251, Estimated correctness of the model 99.7 % 5 chains (251 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 106 A Built loop between residues 75 B and 80 B Built loop between residues 87 B and 94 B 2 chains (263 residues) following loop building 2 chains (263 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2440 restraints for refining 2450 atoms. 256 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2415 (Rfree = 0.000) for 2450 atoms. Found 73 (75 requested) and removed 42 (41 requested) atoms. Cycle 7: After refmac, R = 0.2231 (Rfree = 0.000) for 2475 atoms. Found 48 (74 requested) and removed 42 (42 requested) atoms. Cycle 8: After refmac, R = 0.2111 (Rfree = 0.000) for 2479 atoms. Found 53 (72 requested) and removed 19 (42 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2067 (Rfree = 0.000) for 2508 atoms. Found 27 (74 requested) and removed 39 (43 requested) atoms. Cycle 10: After refmac, R = 0.2014 (Rfree = 0.000) for 2494 atoms. Found 41 (71 requested) and removed 18 (42 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.08 2.25 NCS extension: 0 residues added, 2517 seeds are put forward Round 1: 260 peptides, 4 chains. Longest chain 94 peptides. Score 0.958 Round 2: 263 peptides, 4 chains. Longest chain 94 peptides. Score 0.959 Round 3: 261 peptides, 6 chains. Longest chain 76 peptides. Score 0.949 Round 4: 263 peptides, 5 chains. Longest chain 95 peptides. Score 0.955 Round 5: 261 peptides, 7 chains. Longest chain 77 peptides. Score 0.945 Taking the results from Round 2 Chains 4, Residues 259, Estimated correctness of the model 99.8 % 4 chains (259 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 106 A Built loop between residues 104 B and 107 B 2 chains (263 residues) following loop building 2 chains (263 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2495 restraints for refining 2501 atoms. 311 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2212 (Rfree = 0.000) for 2501 atoms. Found 58 (71 requested) and removed 42 (42 requested) atoms. Cycle 12: After refmac, R = 0.2083 (Rfree = 0.000) for 2514 atoms. Found 39 (71 requested) and removed 38 (43 requested) atoms. Cycle 13: After refmac, R = 0.1999 (Rfree = 0.000) for 2515 atoms. Found 52 (69 requested) and removed 29 (43 requested) atoms. Cycle 14: After refmac, R = 0.1956 (Rfree = 0.000) for 2535 atoms. Found 53 (67 requested) and removed 28 (43 requested) atoms. Cycle 15: After refmac, R = 0.1919 (Rfree = 0.000) for 2558 atoms. Found 50 (66 requested) and removed 31 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.08 2.25 NCS extension: 0 residues added, 2577 seeds are put forward Round 1: 262 peptides, 3 chains. Longest chain 133 peptides. Score 0.963 Round 2: 265 peptides, 4 chains. Longest chain 95 peptides. Score 0.960 Round 3: 266 peptides, 4 chains. Longest chain 100 peptides. Score 0.961 Round 4: 264 peptides, 3 chains. Longest chain 134 peptides. Score 0.964 Round 5: 265 peptides, 5 chains. Longest chain 76 peptides. Score 0.956 Taking the results from Round 4 Chains 4, Residues 261, Estimated correctness of the model 99.8 % 3 chains (260 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 104 B and 110 B 3 chains (266 residues) following loop building 3 chains (266 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2455 restraints for refining 2495 atoms. 253 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2195 (Rfree = 0.000) for 2495 atoms. Found 63 (63 requested) and removed 43 (42 requested) atoms. Cycle 17: After refmac, R = 0.2037 (Rfree = 0.000) for 2509 atoms. Found 52 (62 requested) and removed 42 (43 requested) atoms. Cycle 18: After refmac, R = 0.1952 (Rfree = 0.000) for 2518 atoms. Found 46 (60 requested) and removed 25 (43 requested) atoms. Cycle 19: After refmac, R = 0.1920 (Rfree = 0.000) for 2534 atoms. Found 46 (58 requested) and removed 24 (43 requested) atoms. Cycle 20: After refmac, R = 0.1869 (Rfree = 0.000) for 2555 atoms. Found 43 (57 requested) and removed 27 (43 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.08 2.25 NCS extension: 0 residues added, 2572 seeds are put forward Round 1: 261 peptides, 4 chains. Longest chain 134 peptides. Score 0.958 Round 2: 262 peptides, 5 chains. Longest chain 135 peptides. Score 0.954 Round 3: 260 peptides, 6 chains. Longest chain 77 peptides. Score 0.949 Round 4: 262 peptides, 5 chains. Longest chain 135 peptides. Score 0.954 Round 5: 261 peptides, 6 chains. Longest chain 77 peptides. Score 0.949 Taking the results from Round 1 Chains 4, Residues 257, Estimated correctness of the model 99.8 % 3 chains (250 residues) have been docked in sequence Building loops using Loopy2018 4 chains (257 residues) following loop building 3 chains (250 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2635 restraints for refining 2490 atoms. 536 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2135 (Rfree = 0.000) for 2490 atoms. Found 54 (54 requested) and removed 42 (42 requested) atoms. Cycle 22: After refmac, R = 0.2007 (Rfree = 0.000) for 2500 atoms. Found 51 (53 requested) and removed 34 (42 requested) atoms. Cycle 23: After refmac, R = 0.1965 (Rfree = 0.000) for 2517 atoms. Found 40 (52 requested) and removed 30 (43 requested) atoms. Cycle 24: After refmac, R = 0.1912 (Rfree = 0.000) for 2526 atoms. Found 36 (50 requested) and removed 23 (43 requested) atoms. Cycle 25: After refmac, R = 0.1891 (Rfree = 0.000) for 2536 atoms. Found 48 (48 requested) and removed 22 (43 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.08 2.25 NCS extension: 47 residues added (100 deleted due to clashes), 2610 seeds are put forward Round 1: 263 peptides, 4 chains. Longest chain 133 peptides. Score 0.959 Round 2: 262 peptides, 6 chains. Longest chain 134 peptides. Score 0.950 Round 3: 263 peptides, 5 chains. Longest chain 76 peptides. Score 0.955 Round 4: 262 peptides, 6 chains. Longest chain 124 peptides. Score 0.950 Round 5: 260 peptides, 6 chains. Longest chain 74 peptides. Score 0.949 Taking the results from Round 1 Chains 4, Residues 259, Estimated correctness of the model 99.8 % 3 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 B and 80 B 3 chains (263 residues) following loop building 2 chains (254 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2559 restraints for refining 2501 atoms. 420 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2166 (Rfree = 0.000) for 2501 atoms. Found 48 (48 requested) and removed 46 (42 requested) atoms. Cycle 27: After refmac, R = 0.2044 (Rfree = 0.000) for 2502 atoms. Found 44 (46 requested) and removed 31 (42 requested) atoms. Cycle 28: After refmac, R = 0.1979 (Rfree = 0.000) for 2515 atoms. Found 41 (45 requested) and removed 20 (43 requested) atoms. Cycle 29: After refmac, R = 0.1924 (Rfree = 0.000) for 2535 atoms. Found 39 (45 requested) and removed 25 (43 requested) atoms. Cycle 30: After refmac, R = 0.1905 (Rfree = 0.000) for 2547 atoms. Found 39 (43 requested) and removed 32 (43 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.08 2.25 NCS extension: 0 residues added (9 deleted due to clashes), 2555 seeds are put forward Round 1: 261 peptides, 5 chains. Longest chain 133 peptides. Score 0.954 Round 2: 260 peptides, 6 chains. Longest chain 77 peptides. Score 0.949 Round 3: 261 peptides, 5 chains. Longest chain 85 peptides. Score 0.954 Round 4: 265 peptides, 6 chains. Longest chain 77 peptides. Score 0.952 Round 5: 262 peptides, 5 chains. Longest chain 134 peptides. Score 0.954 Taking the results from Round 5 Chains 5, Residues 257, Estimated correctness of the model 99.7 % 3 chains (243 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 B and 86 B 3 chains (262 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2557 restraints for refining 2481 atoms. 427 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2205 (Rfree = 0.000) for 2481 atoms. Found 42 (42 requested) and removed 45 (42 requested) atoms. Cycle 32: After refmac, R = 0.2049 (Rfree = 0.000) for 2475 atoms. Found 42 (42 requested) and removed 32 (42 requested) atoms. Cycle 33: After refmac, R = 0.1975 (Rfree = 0.000) for 2485 atoms. Found 42 (42 requested) and removed 19 (42 requested) atoms. Cycle 34: After refmac, R = 0.1933 (Rfree = 0.000) for 2508 atoms. Found 42 (42 requested) and removed 23 (42 requested) atoms. Cycle 35: After refmac, R = 0.1905 (Rfree = 0.000) for 2527 atoms. Found 41 (43 requested) and removed 30 (43 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.08 2.25 NCS extension: 56 residues added (115 deleted due to clashes), 2596 seeds are put forward Round 1: 260 peptides, 4 chains. Longest chain 133 peptides. Score 0.958 Round 2: 260 peptides, 6 chains. Longest chain 76 peptides. Score 0.949 Round 3: 260 peptides, 4 chains. Longest chain 133 peptides. Score 0.958 Round 4: 260 peptides, 8 chains. Longest chain 77 peptides. Score 0.939 Round 5: 261 peptides, 7 chains. Longest chain 123 peptides. Score 0.945 Taking the results from Round 3 Chains 4, Residues 256, Estimated correctness of the model 99.8 % 3 chains (247 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 B and 80 B 3 chains (260 residues) following loop building 2 chains (251 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2542 restraints for refining 2456 atoms. 438 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2165 (Rfree = 0.000) for 2456 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 37: After refmac, R = 0.2037 (Rfree = 0.000) for 2454 atoms. Found 42 (42 requested) and removed 18 (42 requested) atoms. Cycle 38: After refmac, R = 0.1963 (Rfree = 0.000) for 2477 atoms. Found 42 (42 requested) and removed 18 (42 requested) atoms. Cycle 39: After refmac, R = 0.1918 (Rfree = 0.000) for 2500 atoms. Found 42 (42 requested) and removed 22 (42 requested) atoms. Cycle 40: After refmac, R = 0.1884 (Rfree = 0.000) for 2520 atoms. Found 39 (43 requested) and removed 22 (43 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.08 2.25 NCS extension: 4 residues added (8 deleted due to clashes), 2543 seeds are put forward Round 1: 263 peptides, 4 chains. Longest chain 136 peptides. Score 0.959 Round 2: 260 peptides, 6 chains. Longest chain 133 peptides. Score 0.949 Round 3: 257 peptides, 7 chains. Longest chain 76 peptides. Score 0.942 Round 4: 259 peptides, 7 chains. Longest chain 124 peptides. Score 0.943 Round 5: 260 peptides, 8 chains. Longest chain 76 peptides. Score 0.939 Taking the results from Round 1 Chains 4, Residues 259, Estimated correctness of the model 99.8 % 3 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 B and 80 B 3 chains (263 residues) following loop building 2 chains (254 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2555 restraints for refining 2497 atoms. 423 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2124 (Rfree = 0.000) for 2497 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 42: After refmac, R = 0.2021 (Rfree = 0.000) for 2493 atoms. Found 42 (42 requested) and removed 23 (42 requested) atoms. Cycle 43: After refmac, R = 0.1938 (Rfree = 0.000) for 2510 atoms. Found 37 (43 requested) and removed 14 (43 requested) atoms. Cycle 44: After refmac, R = 0.1917 (Rfree = 0.000) for 2532 atoms. Found 30 (43 requested) and removed 28 (43 requested) atoms. Cycle 45: After refmac, R = 0.1872 (Rfree = 0.000) for 2533 atoms. Found 38 (43 requested) and removed 19 (43 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.07 2.24 NCS extension: 48 residues added (92 deleted due to clashes), 2601 seeds are put forward Round 1: 260 peptides, 4 chains. Longest chain 133 peptides. Score 0.958 Round 2: 257 peptides, 7 chains. Longest chain 67 peptides. Score 0.942 Round 3: 258 peptides, 7 chains. Longest chain 84 peptides. Score 0.943 Round 4: 258 peptides, 6 chains. Longest chain 67 peptides. Score 0.948 Round 5: 254 peptides, 6 chains. Longest chain 84 peptides. Score 0.945 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 256, Estimated correctness of the model 99.8 % 3 chains (246 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 74 B and 80 B 3 chains (260 residues) following loop building 2 chains (251 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19227 reflections ( 99.63 % complete ) and 2104 restraints for refining 2062 atoms. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2678 (Rfree = 0.000) for 2062 atoms. Found 21 (35 requested) and removed 0 (35 requested) atoms. Cycle 47: After refmac, R = 0.2519 (Rfree = 0.000) for 2062 atoms. Found 5 (35 requested) and removed 0 (35 requested) atoms. Cycle 48: After refmac, R = 0.2421 (Rfree = 0.000) for 2062 atoms. Found 6 (35 requested) and removed 1 (35 requested) atoms. Cycle 49: After refmac, R = 0.2352 (Rfree = 0.000) for 2062 atoms. TimeTaking 52.1